-Check the vacuum lines to the modulator on the front of the trans -that could be your RPM issue. If that line is leaking, the modulator will think you have a lot more throttle than you do, and may not upshift properly, or as Jon said, it may just not be locking up the TCC. How does the fluid look? If it smells burnt, or is more purple or brown than red, that could be the beginning of the trouble...
-5-speed swaps still have their problems for the newer body, since the mounts are kind of an issue -there were no '96 V-6 five-speed cars, for instance. That is the route I would go though. My '95 Z-26 is slated for it, who knows when that will ever happen though? I might have a spare five-speed shift-plate though, I had two of them with the car when
GTiIndy took it, but a lot of badness happened to that car while it was out of my sight, so I can't say if all of those parts are still any good -if you can't find any others, shoot me a PM when you get to that point and I'll see if I can help out.
-6-speed... Well, there are two of them on here, I have the first one, and they are done very differently from each other. The '06 tranny, like I have, has a great gear-ratio, but is known for synchronizer issues. The '07 trannys, like Shawn's, may be a less problematic tranny, but have sucky gear ratios, making a five-speed a better unit unless you need the torque-handling capabilities of the F40 six-speed (I think it is the highest-rated manual transaxle GM has produced to date). Mine cost me ~$1000 and way too much time and trouble, and rattles like a Cummins diesel at idle. If you cannot do welding and machining, plan on doubling or tripling that cost. If you have questions, let me know, you can also find a lot of info from Joseph U. on Pennock's Fiero Forum -he was basically the F40 swap pioneer IMO.
-The 3500s use electronic TBs, so you need to find a compatible cable-operated TB (I think it is the LX5 DOHC 3.5 "Shortstar" found in some Auroras and Intrigues, several people here know for sure). Custom exhaust work, too... That external crank-trigger is the big problem though, so if you get that figured out it is all downhill from there.
-3400 swap is bolt-n-go for your car. No fuss, no muss. Just ditch the plastic GM LIMGs for steel and rubber units, you will be happy with it for a long time. Doesn't even need a tune, unless you want that extra edge a good tune can get you from any engine.
I like the GT/Indy/Z-26 spoilers too. Kind of a plain 'bump', but it fits the body lines nicely and is understated. I don't much care for the Beretta's back-end naked, but it is all just personal preference. That spoiler shouldn't be too hard for you to find.
Congrats on finding the car, man. I was beginning to lose hope for you!
It sounds like it is in good hands, too.