Well you actually have two seperate swaps going on there. The auto>>>manual swap and the 2.8>>>3800 swap.
Both are well documented here so I won't go into too much detail. My experience is limited to the supercharged 3800. All the following should still be the same though.
Auto>>>ManualNew pedal assembly
New clutch master cylinder
New hardlines under the floor
New shifter and surround trim
New shift cables
Steering column different - Auto has a cable to allow the starter to work when in Park. Manual has switch on pedal.
...and of course the transmission itself and the axles
Nothing needs to be reprogrammed that wouldn't normally need to be reprogrammed for the 3800 swap.
2.8>>>3800With a manual, you'll need a Camaro 3800 flywheel.
You'll have to machine it down to 0.840 inches thick, if I recall correctly.
Stock trans mounts will be used.
New mounts and dog bone for the engine will have to be fabricated or bought.
The 3800 wire harness has to be reworked to interface with some of the Fiero connectors.
The PCM has to be reprogrammed.
New exhaust has to be fabbed up.
Coolant hoses will be needed but aren't too difficult.
Some people modify the Fiero thermostat housing to work on the 3800 but I just used the stock 3800 termostat housing. Burping the coolant
can be a biatch though.
The stock mounting location of the alternator won't fit under the deck lid. Modify the deck or move the alternator.
The Fiero fuel pump needs to be replaced by a better fuel pump.
I'm sure I forgot something.
You might consider sticking with the 4T60 or a 4T65 automatic rather than swapping to a manual.
For what it's worth, my next one will have an automatic.
The 3800SC has enough balls that even an auto should be fun to drive. I find the manual to be a negative in the Fiero because the gear ratios are all wrong and I'm always worried about breaking the case in half if I beat on it too hard.
[This message has been edited by 2002z28ssconv (edited 04-25-2012).]