Yes and No, yes you can use an 88 motor, its actually a better engine than the 86.  However here are the differences.

88 is internally balanced so you MUST use the flywheel/flex plate from the 88 motor.  If you put your 86 one on it will destroy the motor.

88 has slightly different sensors, so you will need to use your 86 sensors.  I can't remember all the ones that are different, but I know for use the Oil pressure sender is different.

Exhaust down pipe is totally different so you must use the exhaust Y pipe from your 86.     The 88 ECM is different, however your 86 one will run it just fine. 

Injectors are usually better in the 88's, and are plug and play with the 86 harness so no need to worry there.

I think that about covers the odd changes.    I bought an 85 Fiero that had an 88 motor installed in it, everything ran fine.    I own an 88GT and an 85Gt and an 87GT which I routinely swap parts around.

The 4spd and 5spd flywheel for any given year is the same.  So you can use an 88 5spd flywheel on your 4spd without any issue.  I believe there is also a 4cly Sunfire flywheel than can be used on the 88 V6  motors as well.   I am sorry I don't have the interchange info handy.  I think Dr. Fiero has the part numbers so hopefully he replies to this thread.  

         In todays day and age trying to find a clean rust free frame is next to impossible unless you find someone like myself that has owned the car since near new and took care to not let rust take hold on the car.     Most any "cheap" car is going to be hard, wait, wait wait a min.

                 Go to craigslist as quickly as you can, find an 87SE for sale in Chilliwack.   Its $550 I know the history on the car and it even won some shows locally, however in the last 3 years it has passed hands several times and been sold for less and less each time.   The person that took care of it, actully did take good care of it.  Its a black 87SE V6 Auto car.  Chin Spoiler, Tinted front markers, nice paint, or at least it use to be nice.    To my knowledge the engine is blown and the brakes are shot, but if you have all the donar parts at your disposal to fix it up, you might come out really ahead of the game.

Here are pics from back in the day,

Mizers 87SE  in Chilliwack

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Maybe I should make a new topic for this, but for now, I'll put it in here.

This is a very nice 86SE

This is an 85GT

Both cars are 90% identical from the factory, same body, same ground skirts, same nose, rear bumper and hood and deck lid are the same.  Same headlights, only real difference is the speakers were in the seats on 85 cars and in 86+ they moved them to the B pillars.

     Same 4spd's you get the picture.

In ICBC's eyes the 85GT is worth 2-3 times as much as the 86SE simply because the 85 was a GT.  When I was in my fender bender in my 85GT a few years ago, they valued my 400,000km 85GT with at that time a stock V6 and stock suspension at $5000, and even cut me a cheque for $2500 for repair costs.  (I had them pay the claim out to me for the repairs - at my cost the repairs were only $250, their estimate was $3000 for repairs)  Thats one of the "coughkeptmyvinplatescoughcoughwithregypaperswcough" reasons that I'll part out an SE due to much less damage than I would part out any GT.   With the value of our cars rising every year even ICBC is paying out bigger and bigger numbers for Fiero's.  Always keep all your receipts for everything you do. 

Make sure you spray down rusted bolts/nuts with plenty of PB Blaster and let it soak in overnight at least.

garrym wrote: i noticed the brake fluid cable from the front connects to the engine via a large cilinder thing, the 88 engine doesnt have this, i will be swapping it over. any suggestions yet?

???

Are you referring to the clutch slave cylinder on the transmission?

Clutch fluid, brake fluid... same stuff.

If you've got a hydraulic line going to the engine/transmission, there's only one place for it to go... the clutch slave cylinder.