I would run a single port 96-98 v6 motor they are DIRT cheap my friend got a good shape one for 80 bucks.... then simply build it with boost and .... if you do it right you should be pushing 500rwhp
For supercharging, I wouldn't think to use a pre 89 3.8L V6. Even then it's debatable as to the worth. Those engines are okay with decent boost levels, but have inherent problems with high boost, particularly in pre 89 blocks. I'd rather a 2.3L Turbo 4 banger myself. It's definitely more capable from all I've seen in the past.
I don't know the years of each V6 used, but Ford certainly used the 3.8L in Mustangs from '84-86 models. I'm sure the 2.8L was used as well, but prior to '84 I'd think, and maybe before 83 as well, depending on when the 3.8L was actually used.
the 2.8 can take gobs of boost, they are strong like bull
little history, The 2.8L is based on the 2.6L which is based on the 2.3L which dates back to the early 70's. The 2.8L is one version of the famous Cologne V-6 whichalso spawned the 2.9L and the current 4.0L that is available in the Ranger and Explorer. The new 4.0L SOHC uses the basic Cologne
"architecture" too.
One thing to consider, and I don't know this for a fact, but I've heard, that the kmember is different in the v6 Fox Bodies versus the other 4cyl/V8 cars, that's part of the reason they dropped the six was cuz of a different part used to assemble the whole car. So that also means you may have a hard time finding motor mounts which I think are pretty hard to find, but I don't know for sure, I've thought about the same swap myself, but with a factory V6 car, and drop in the 99 newer engine, and controls. You can supercharge a carbed motor, ProCharger makes a system for sure, you could use the same setup for the 94-04 V6s (should use all the same brackets) dimensions between fox bodies and fox4 bodies are pretty close so things would come real close to fitting identically. Then put a carb hat on top of the carb. Should work, hell as cheap and plentiful as V6's are you could afford to blow a couple apart, hehe.
a stock 99+ v6 can take 14~ psi or more but... its all in the tune, I wouldnt run more than 11 psi with out forged internals then heck .... it will take just about what ever level of boost you put on it wiht in reason of course.