The conversion is quite easy, only time consuming. If you have a donor car, get everything to make the transition easier. There is a large bundle of wires that runs on top the pedals that must get moved. That can be the biggest nuisance. It can be done in a weekend though, I just went through this recently. There are a few threads on here with pics so that'll help you out if you get stuck.
In my '87 SE, the auto to manual swap cost around $2k and took about a week. But I was working on it in my spare time, a few hours here and a few hours there. And I bought a lot of new parts (aluminum flywheel, Spec clutch, stainless steel clutch hydraulic line, new axles, rebuilt transmission, Rodney Dickman shifter cables, etc).
By far, the biggest headache was swapping out the pedal assemblies. You have to lay on your back in the driver's side footwell and finnagle the pedal assembly past a fat wire loom that can't be moved out of the way. Also, removing the tranny cooler lines and installing the clutch hydraulic line was kind of a pain. I ended up chopping the tranny cooler lines into several pieces to get them out. The Fiero Store stainless clutch line came in several pieces, that you attach together. That helps. But threading the line around the front suspension crossmember was still a pain.