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I bet your master cylinder throw is not adjusted correctly. Judging by the set nut being in the wrong location. If the throw isn't set properly the valve in the master doesn't allow flow back to the master decreasing the distance that the clutch will disengage the next time you apply your clutch pedal.

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Grab a friend and follow the master cylinder setup process outlined by these guys just following the bleeding process in this video:

 

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thanks ill give it a shot, the nut you circled in the picture is the locking nut to keep it tight, not the adjustment nut, although in that picture it adjusted to be as far out as possible
Just remember that the rod's throw adjustment isn't like it is on a cable clutch adjustment that can give you an adjustable grab point. The rod's throw adjustment is for the valving inside the master to allow flow in either direction. If it's incorrectly set you will effectively have a one way valve with a rock hard pedal or a soft pedal. Anything in between may work intermittently.

Since it is set to be as long as possible, the valve isn't closing to pump pressure until about 25% or 33% of the clutch pedal distance. That means you have that much less distance to build pressure and fully disengage the clutch. Adjust it with a friend like in the video and you'll get back all the pressure and distance you need to get in and out of gear without any issues.
 
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Could be a faulty or incorrect master cylinder if you're unable to push back on the slave. The valving or rod may not be correct. Do you happen to have a photo of both the new and old master cylinders?

I replaced my master cylinder which was slightly different than the OEM for my V6/6Speed from a cheap "OE" manufacturer. I tried it regardless thinking it was a different design revision or part update but I could never get it to work right. I decided it was likely from a V6/5Speed or L4/5Speed and tossed it out. Never figured out why it was different though. I ended up sourcing a used OEM master cylinder and it solved my problems.
 

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Try shortening the rod adjustment as far as you can to see if it stops letting you push it back in. Infact is there ever a point while slowly pressing down on the clutch where it stops? That's a good indicator of how far you need to shorten the rod. If there is no point which it stops then you may have a faulty or incorrect master cylinder.
 

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There should be a point while pressing down on the clutch pedal where you won't be able to push back on the slave cylinder because the valving inside the master cylinder is only allowing flow in one direction. On a normally functioning car that should be within about 0.25" from the top of the pedal location. If you have to push on the clutch a fair amount before it blocks reverse flow from the slave cylinder this is a good indicator it's the wrong master or could be damaged. Could also be an indicator it was never bled properly.
 

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Try shortening the rod adjustment as far as you can to see if it stops letting you push it back in.
I made a mistake with this advice. I meant that you should adjust the rod longer until the slave stops pushing in. Then you shorten it one to two turns so that you can push back on the slave to return fluid back to the master reservoir.

Essentially you have a variable one way valve in the master cylinder. You want to adjust that master cylinder rod so that the valving allows flow back to the master reservoir with the pedal all the way up in it's resting position. You may have to lift the pedal by hand or foot to it's resting position if the clutch isn't resetting it's position for you. You want the valving the block that flow with about 0.125-0.25" of pedal travel so that pressure builds to disengage the clutch when fully pressed to the floor. If the master rod adjusted too long, the valving will block flow back to the master reservoir at the pedals resting position preventing clutch engagement when the pedal is released. Then if it's adjusted too short it may build pressure too late in the pedal travel to be effective enough to disengage the clutch. There is a fine line of adjustment where it needs to be to function properly.

Wait your saying when I'm pushing the slave back to see if the valve is closed I should have someone press on the clutch pedal during that time? That's not what I understood from the video and would make sense as to why I can't find that point
You don't want to press on the clutch pedal while you are doing the procedure from the video for the final adjustment. What I proposed is as a simple test to see if you have a point at all in the pedal travel where the master valving prevents you from pushing the slave rod in. IE if the master rod is adjusted to the shortest or longest and you can still push the slave rod in... then have someone softly press on the clutch pedal until the valving in the master prevents you from pushing on the slave rod in. If the distance you have to push the pedal is significant like 50% pedal travel, there is no amount of adjusting the master rod that will fix this and you should look into obtaining another master as a last resort.
 
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The switch is simply to tell your ECM or BCM that you are depressing the clutch. One purpose is to turn off cruise control immediately if the clutch is pressed instead of waiting until the bottom of the clutch travel like it does for starting the car. But that switch does nothing to the master cylinder.

Once you have found a point which the valve blocks flow, shorten the rod by about 1-2 turns and that should set you just right. If you still have problems then you may have a faulty slave, faulty fork or faulty release bearing.

Another problem may be the clutch disc. Are you certain you installed it the right direction? Was it a sprung or rigid disc? The disc may need to be worn in a little bit more so it doesn't catch while fully "disengaged"
 

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I'm in the process of pulling the trans off now, I'm positive I have it adjusted properly, it's on the right way, sprung, I put the same clutch in a buddy's car and he never had issues with it not going into gear during break in so I'm just gonna check everything and then probably replace the fork and try it again
While you are in there, measure the depth of your ark flywheel friction surface to the flat area the clutch cover (pressure plate) mounts to. I'm curious if it differs from my Fidanza flywheel which is a common pairing with Clutchmasters discs.
 

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The 2nd pic is the correct depth but the reading on your caliper is nearly 3inches or 70mm which can't be right.

I measured my Fidanza depth and it was 8mm or 0.32". My thoughts were if you depth was smaller than that, it's possible that the CM disc may need to be worn or flywheels.needs to be bedded in more to function normally.

What about the torque used on the clutch cover/pressure plate bolts? If you over torqued them you could have trouble fully disengaging the clutch.
 

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i'll remeasure the 2nd pic, if I remember right i torqued them 4 lbs over spec because it was something like 14 foot pounds which i thought was dangerously little
14 lbs is right for the bolt size and thread type. It's not about the work the bolt is doing, it's about the strength at which the bolt, threads or material you thread it into will yield and start to break. You size the bolt and threads based on the material and holding force you require. You don't need to go higher 14lbs and it will hold no problem since it has lock washers. My last clutch I torqued to 14lbs and it lasted 60k miles no problem.

also I thought about that but I have almost 200 of the 600 break-in miles done so I figured it would be past that point by now, and I did a CM fx250 and fidanza flywheel on an Acura RSX and it never had any issue like this at all, always smooth easy shifting
It took me over 1500 miles to break in my last clutch because I drove mostly highway miles on a 1000 mile round trip as soon as the new clutch was installed. (Literally less than 12 hours after the clutch was completed) It really depends on the type of driving you do. They recommend stop n go traffic for the break in period for quicker results. You can subtract any long highway miles you drive since you aren't actively engaging/disengaging the clutch enough to bed in the materials.
 

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fair enough most of the driving was highway but I was trying to do as much stop and go as possible, ill remeasure the distance for the flywheel and pressure plate, if it seems very abnormally off then I will buy a fidanza flywheel to replace the Ark, if its fine then ill just re-torque the bolts, replace the clutch fork and TOB, check over everything one more time and then put it all back together
I'm sure the ARK is fine. I was just curious what the depth would be from the flat mount point on the highest point of the flywheel. It's always possible that quality control was not so great the day they machined your flywheel. Although that's very rare for something like that to slip past QC on a precision part like that.

Looks like you have plenty of clearance that it shouldn't be binding on the disc while the clutch pedal is to the floor. I would continue troubleshooting the hydraulics if I were you.
 
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To be clear, these were the dimensions I was measuring at 8mm or approximately 0.315-0.32 inches. Anything smaller than that may cause you grief.

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Sorry my clutch release bearing came loose. If I recorded a video it would only go one way without resetting. It would have to wait until I get my new clutch installed later this winter.
 

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Is it possible that you have worn out synchros? Maybe this problem developed more as you were troubleshooting these last few weeks/months and grinding in and out of gear.

I occasionally have a little trouble getting into reverse when my transmission is cold and it depends on what gear oil I'm using. Have you tried the Redline LSP cocktail at all? Which gear oil are you using currently?

Did you replace the release bearing sleeve that bolts to the transmission around the input shaft? If the grooves created by the release bearing are deeply worn it can restrict clutch disengagement near the top end of it's travel.

Surprisingly tire pressure plays a small role in grinding through gears while moving. If there is an imbalance in wheel speed due to tire wear or tire pressure it can cause a slight bind in shifting. This was something I discovered around my 40k mile mark when I started grinding into 2nd and 3rd. Even tire pressure would alleviate it to some extent. This is only affects grinding while rolling however. I presume you are experiencing grinding into 1st and reverse while standing still? Downshifting to 1st while rolling will grind unless you are traveling 15mph or less it seems like.
 

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Wow! That is so weird it made almost no contact on the flywheel. Just enough to discolor the outer part. You had the correct side of the FX250 facing the flywheel from what I've seen in person. I also have an FX250 where I test fit to a Fidanza flywheel and it would only attach one way correctly. There should be enough of a recessed area in the flywheel for the non-flat side to face the flywheel. Do you see any obvious contact anywhere else such as the bolts or inner area where the friction surface begins to taper into the bolts? How do the splines look on the transmission input shaft?

On the Valeo install I believe the flat site towards the flywheel only applies to the dual mass flywheel with rigid clutch disc. The flywheel has no clearance in the middle where you do on the single mass flywheels so the slightly raised side of the Valeo rigid disc would face the pressure plate. If you are referring to this video at 466 seconds then that ONLY applies to the rigid disc and dual mass flywheel combination.

So basically, single mass flywheels get the flat side to the pressure plate while dual mass flywheels get the flat side to the flywheel.
 
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And just for clarity sake, this is the direction the FX250 is supposed to fit (flat side up to pressure plate, raised side down to flywheel) and what the inner dimensions are for clearance. The flywheel inner diameter of the Fidanza is approximately 5.75" and the disc needs a minimum of 5" to clear. I imagine if your flywheel has a smaller inner diameter that's close to 4.9" then you might be making contact there. Otherwise I do see a little wear by your disc's springs that might be making contact with the flywheel bolts.

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