Your first issue is going to be finding a manual transmission flywheel for a Series 1 SC. Series 2 flywheels are easier to find. I have never heard of a FWD 3800 Series 1 manual flywheel. Let alone one for a SC. Except for a expensive custom made one. It would be cheaper to keep the automatic from the car.
Your next issue is going to be the PCM. The 95 and 96 PCMs are very buggy to have flashed. The 94 PCMs had eproms but suck. And I haven't seen any bin files for 94-96. Your best bet if you stick with Series 1 is a 92-93 PCM. The MAF sensor will have to be replaced with the older MAF. IF you decide to do automatic, the internal wiring in the transmission will need to be modified.
I currently have a 85GT with a Series 2 SC. Using a 1993 16141470 PCM. The transmission was from a 1995 N body with very simular internals to the C/H body. Still had to modify the internal wiring. It started with a 1993 3800 SC that had sat for a looong time but had only 70,000 on it. Ran great for about 3000 miles then spun a bearing. Found a chunk of rust that had came from an oil galley. I didn't have problems with clearance, but I had made my own mount brackets. I went with a 4 point mount setup, doing away with the dogbone. That also gave me more room for the oil filter. I'm not running A/C, but there is still room for it. I put the alternator where the power steering is on the Buick. When the engine went, I found a Series 2 with 90,000 on it. Had to rework my alternator, tensioner brackets, Exhaust and change the wiring to except a 1998 MAF. But I am still using the 1995 transmission and 1993 PCM. For the axles I used the axles that came with the V6 N body (Grand Am, Skylark, Achieva 93-95 with 4T60e) transmission. The outboard joints worked with the Fiero hubs. I just had to change the right shaft part of the axle, with one from a 3.1/4T60e W-body to change the lenth.
I would suggest getting a spare cradle so you can mock everything up on it before doing the swap. When I did mine, the only thing I had to contend with after was the wiring. But I was able to drive it home.
Due to 2 collisions, The 85 will soon be taken apart. I currently drive an 87. I will be removing the complete drive train, including the cradle, wiring, fuel system etc. from the 85. Over the next few months, I intend to have everything completed to make it plug and play for the 87. Really the only things I need to do are, redo the exhaust and take care of the rats nest of wiring that goes under the consol. I am determined to be able to unplug/plug in. If I can con my wife into letting me use her camera and I finally learn how to post pics, I might share.
[This message has been edited by cmechmann (edited 02-19-2015).]