Many say that it's less expensive to buy a car which already has the transmission you want than it is to swap it. My knowledge is mostly with the V6's but the a lot of the same principles apply here. One thing to be very aware of, is that there was a change in the BETA motor (again I'm a V6 guy so I'm not 100% on this) where they changed from a MAP sensor without CVVT to a MAF sensor with CVVT in the early 2000s. If the donor car has CVVT and your destination car doesn't have CVVT, or vise versa, then the ECM/harness swap will not work. You will have to swap the whole engine, engine harness and transmission with it.
It's not very clear by your run-on sentence whether you are swapping manual to automatic or automatic to manual... but it's going to be the same headache either way. For example, to swap automatic to manual successfully you need several parts from a manual Tiburon:
Manual trans
Manual trans engine harness
Manual trans ECM (Auto trans ECM might work but you'll likely have a TCM and a transmission speed input/output sensor check engine light then fail your inspection)
Gauge cluster (may differ between automatic and manual cars)
Hydraulic clutch master/slave system
Shift cables and shifter assembly
Manual trans driver's side CV axle. (I'm not sure about the 2.0 but it's possible that the stub shaft and passenger side is required as well.)