Never done it, so I am not speaking from experience, but I can say that many others have done the "Top Swap" sucsessfully. Unfortunatly, and you aren't going to like this much, the long block is a No-Go. The heads are different. The supercharged heads are drilled for injectors while the NA's have them in the intake manifold. The heads are actually the same casting. So, no matter what, you will have to remove the heads to do the swap. I suppose you could have the heads machined for injectors, but its hardly worth the price if you are using a full donor engine anyway.
People who have done the top swap wind up with a more powerful engine then a standard L67 due to higher compression pistons. The bottom end doesn't quite have all the bells and whistles of an L67, (better rods and pistons) but no one complains of the NA's bottom ends letting go under supercharged service.
You will need:
Heads
Head bolts
Valve Covers (with hardware)
Valve Cover gaskets
Intake maifold
Lower intake gaskets (Get ones for a Series III, they are FAR better)
Supercharger base gasket (with the 2 O-rings)
Throttle body gasket (if you take the throttle body off for some reason)
Supercharger
Fuel Rail and hardware
Injectors
Throttle body (often it's still attached to the SC, includes MAF)
Supercharger Boost Bypass Solenoid and Actuator
Wiring for Bypass valve
Front Cast Iron GTP pulley bracket (with idler and tensioner)
Supercharger Idler Aluminum bracket (with idler pulley)
Supercharged harmonic balancer
Supercharger Belt
Supercharger mounting hardware
2 Bar MAP sensor and mounting bracket
Things I am not sure about:
EGR tube (if desired/required)
Heater Core water outlet
Main water outlet (usually a modified V6 Fiero Thermostat housing)
ECM (don't know if they are cross compatible, Im betting they are, but the programming must be different)
Coolant Temperature Sensor (it's different from SC to NA, The SC has an integrated Dash Board Gage sensor, NA has it seperate)
Ignition Module and coils (someone told me they are different, but I'm still skeptical)
Fuel pump (you need to have a good one for the SC'd application, So if you install a good one when NA, then you won't need to upgrade later)
Thats all that I can think of off the top of my head. Obviously, It makes a whole lot more sense to just swap in the 3800 SC in the first place. But its not like it's out of the question. It's also a lot easier to swap the whole engine down the line if a NA 3800 was already in place, just making the wiring modification for the Boost Bypass solenoid. Even that isn't required, But I reccomend using it. And of course whatever ECM stuff is needed. Bottom line, its the same amount of work, and the same modifications to the car to go SC, or N/A.
To the best of my knowlege the exhaust outlets are cross compatible between the two, so you could keep the same exhaust if you go that route. Most people opt to use the stock exhaust manifolds, and make a very short and tightly wound exhaust that comes straight out of the factory exhaust outlet. Many don't run catalytic converters, and quite a number of them cut out the bottom section of the trunk below the shelf to make room for the exhaust. Headers, like the ones West Coast Fiero sells, are a fantastic option for those wishing to keep the V6 Fiero style routing of the exhaust. In my opinion, this also produces the least unplesent sound, as 3800's have a bizarre sound anyway

Other headers made are for FWD's, and typically requre removal of the bottom of the trunk. There are many different ways you can go about this, and quite a number of threads floating around this forum about them.
So if you are dead set on SC'ing the motor later on, Better plan on getting a whole motor and just swapping it in now or later. If you feel you are mechanically frisky and aren't fabricationally challenged, you can turbo the N/A motor and have one heck of a fast car, potentially on a budget.
In before DH