Running GM DIS or ford EDIS off of the MS is actually a simpler way to go than direct coil drive like a stock 12v. If anything, you will get better spark out of the GM DIS setup. I personally use a Ford EDIS and GM DIS coils at the moment with little issues.
The exhaust, passenger motor mount and MS are probably your biggest hurdles although there are a few other compatibility issues you may want to look at or consider:
1) are you going with or without power steering? the pumps are quite different between the other 6G7x variant motors. However you can easily mate a motor specific pump to the chassis specific rack by taking the hoses to a hydraulic shop and having them mate the needed hoses together. the PS pump doesn't produce as much pressure as what the hydraulic couplers are designed to take so failure is minimal at worst
2) A/C - do you want it or not? this is also an engine specific thing, however, you CAN get some A/C shops to couple the A/C hoses to the newer compressor and you should be able to use the stock hi/lo pressure switches and the wiring for the compressor clutch.
3) exhaust - If i read your posts right, you are going to use the stock manifolds, correct? AFAIK
there aren't any aftermarket headers- specifically for the kia 3.5 DOHC. However, if the ports are the same as the 3.0 DOHC, you could probably get a set of non-turbo DOHC headers for the 3000GT and "make" them fit with a saw and welder.
4) clutch - I never actually got to drive my 24v 3.0 with an OEM 12v clutch, however I agree that it should hold up for daily driving and some mild to moderate beating-on. If you start getting clutch slip, then it's time to upgrade. OR get a better clutch from the beginning. a TU kevlar clutch should hold fine and give near stock feel.