The problem is you've got some many band aid "fixes" trying to get a reflashed stock ECU to handle all the mods you've done. I'll start with some of the obvious issues I see:
1) Your running a much larger intake pipe with I'm guessing some of recalibrated/hacked MAF sensor that can measure the flow of 17+ psi. The problem with that is that the stock ECU even in reflashed form was designed for a certain voltage to flow range. Putting a larger MAF means adjusting the rang to fit the needed higher flow rate. So say the stock ECU has a max capability of 16 MAF load cells that correlate to certain flow rates. This may work great for a NA set up but now you've added 17psi of positive pressure in the mix. The problem arises when you need a MUCH broader range of load vs volt load cells but your capped at the max 16 the ECU can support. This can leave you with pretty large gaps in the tune in the low to mid throttle range depending on how the scale was tweaked. NGM tuned most of his reflashes for WOT running without much care taken with the other load areas of a map.
2) You mention using the J&S safeguard. Again this is a band aid fix for improper tuning. A proper reflash would've accounted for all the load variables and adjusted timing accordingly. The Hyundai ECU doesn't like to have its timing externally messed with so this could be causing issues as well.
3) You mention the NEO being installed. Yet another band aid variable added to the mix. NEO's are "OK" with low boost setups where you don't have to pull too much MAF voltage out to tune in slightly larger injectors. Are you trying to use the NEO to help clean up a poor reflash or you trying to go above what the reflash was intended for?
4) You mention you have a AEM wideband. Is it only one wideband? With my Haltech Elite I've seen tune variances between banks of up to +/- 15%. with only one wideband you would have no way to know if a particular bank is running lean. Not a good idea.
5) Ask yourself this question. If all the money you've invested thus far worth limping along with bandaid fixes that could potentially destroy your very expensive motor?
Yes, the car has a 4" intake and Pro MAF on it. NGM called it the big air kit or big induction kit, can't remember. We can all agree that TC wasn't a good tuner and that the reflashes were half ass. There's no way to know exactly what he did, other than it drops into open loop at around 20% throttle and dumps fuel.
It sounds like you have some experience with tuning the factory ECU? I don't, although I do understand the concepts and terminology from my auto technician days. I did fix one that was glitching out due to improper MAF voltage. I saw other people on the boards complaining of the same issue I was having, which makes me think there were more widespread issues with ECU tuning than we were lead to believe.
As of right now, fuel pressure is at factory spec, and the Neo and J&S are zeroed out. It's not that I've been limping along the car as much as it's just been stored for many years. I'm just looking at the way forward. I could possibly utilize the Neo to clean up the fuel curve a little, although as you say, it's a total bandaid. It's a remnant of my Alpine / 290cc injector days.
Have you had a chance to play around with a J&S at all? I'm just wondering where you developed your 'bandaid' opinion of that unit? It's got some capabilities that I'm hoping to utilize, even after I go standalone.
It's interesting that you bring up the banks differing. There are ways to tell without a wideband on each bank, although it's not ideal. I will look into this.
You bring up some valid points. Thanks for weighing in.