I know that I'm pretty much a newbie on here, although I've been reading articles here for many years, but I'm gonns drop my 2 cents into this conversation...
I'm building an 85 SE. The sole reason I bought the car, was because it has a 1pc Targa roof, complete with the mounting brackets on the luggage rack to stash the roof panel should you choose to remove the roof while out on the road somewhere... other than that, the car was a stripped down lump of crud... powertrain was removed, along with interior, steering column, fuel tank, and the biggest PIA, the wiring...
Now other than using the broken front pass. fender for some color testing trying to decide on an eventual color scheme for the car, as well as stripping most (at this point) of the SE triple bar pinstripe pkg off the car, and cleaning the gobs of silicone used to seal the targa when a previous owner couldn't get it to seal properly, I've done no actual physical work to this car yet...
However, I have done literally thousands or hours of research, some here, some on other sites, and some in person through gm dealers and performance shops and parts stores...
Now, to give people an idea, the plans for the car have stayed fairly consistant from day 1: Aero body, keeping the notchback, going with a set of Archie's Integrated rockers, skitime style chin spoiler, and going with a full body (including body kit) color-change paint job, in the red/purple/copper...
powertrain will be a series 2 (or preferably 3) 3800SC, on the F40 tranny, and upgraded brakes. I may lower the car by an inch, but no more, due to our extremely poor local roads. I have a set of extremely limited production 17" Focale rims, and Falken tires that I'm using on my 86 SE V6 auto that I'm daily driving right now, but will be going on the Targa when it's ready...
Now the point of this project that applies to this thread is a couple of things...
Syn, biggest advice I can give you is this: do your research, get yourself very well informed, and then decide on your engine/tranny combo that fits your needs and budget, and stick to it... Everybody has their opinions and preferences, and most of them will be different from each other's and from yours, but the thing that matters is that it's your car, you will be the one driving it, and in the end, you are the only person that you have to worry about satisfying with this project.
I made the choices I did for numerous reasons:
3800SC: reasonably compact size, minimal weight gain over the stock 2.8, excellent base power specs (especially the exceptional very low RPM torque), and very high fuel mileage capacity. My donor car (1993 Bonneville SSEi) used to get 32 mpg, on cruise at 75mph, and that's in a full size weighing in at around 3800lbs... there's no reason that with the much smaller and more aerodynamic body, and the 1000+lbs less weight, with the right gearing this motor should get much closer to the 40mpg mark. The other reason was the relatively simple install, with no major and relatively few minor structural changes required to put the motor in the car... The other consideration to consider was the wild performance improvements avail. for the motor WITHOUT HAVING TO OPEN UP THE ENGINE... even the series 1 that I'm starting with for the time being can be pushed over the 300hp mark with bolt on parts. The deepest I will have to go is removing the valve covers to change the rockers (1.7/1.8/or even 1.9 if you wanna get really crazy, lol).
And the last reason, and this was purely based on my opinion, I've always loved the sound these motors make when you lay into the gas pedal. There's nothing like the look on a mustang owner or ricer's face when they step on it figuring they're gonna blow right by you and your "little old 4 or 6 cyl", only to hear that brutish Whine kick in when you decide not to let them, and that big displacement-6 cyl howl as you walk away on them and there's nothing they can do about it, lol... (although the sound of a V8 growl coming from a Fiero makes for just about the same look, lol)
F40: It's all about the gearing and torque capacity. I've had more than my share of imports and small cars with small motors, and I won't complain, because they've all treated me very well, and stood up to some brutal abuse over the years, and I've even done my share of "shock treatment" when my little s#!t-boxes embarassed a vehicle with considerably more potential, but the one thing that's always annoyed me is high rpm's. There's nothing more annoying in my books than getting out on the hiway with my old 89 Chevy crewcab, and listening to the 350 TBI howling away at 3000+RPM required to do hiway speeds for hours at a time... not to mention the fact that if I go over 65mph, I automatically lose 2-4mpg+ because the motor reaches a point in the fuel map where the mixtures change drastically to compensate for the high RPM's...
That was part of the reason behind my choise in motor, and an even bigger part of my choice in tranny... The 2.8 is comfortable doing sustained cruising between 2500 and 3000 RPM, and my 86 Z24 with the identical 2.8 and 4-spd Muncie as the Fieros did excellent as far as power, torque, and fuel mileage, but it was in the same boat: 3000RPM in 4th at 60mph, and if you keep a stock fiero tranny, then whatever motor you use, you will be stuck with the same issue. Now it's pretty much elementary automotives that given identical cruising conditions, the smaller motor will nearly always make better fuel mileage than the larger, however, the trick to the 3800's whether SC or NA, is to get the cruising rpm's down... a friend of mine was able to get 38+mpg in an 87 Bonneville SE with a N/A 3800, and that car cruised at 1400rpm at 60mph... not to mention, I have seen that car at 180+mph(do not try at home, as speeds like that are only for the insane or stupid, lol)
The biggest reason I chose the F40 was the fact that it had a very wide gearing... it has the short gears for starting out or for racing (of which, if you're running this setup, you're better off to start in 2nd at the track anyway), and you still cruise down around the 15-1600 range at 60mph, which is nearly optimal for fuel mileage on that motor... and the other big reason is the fact that the tranny is rated the highest of any of the manual transverse GM trannys... I'm not going for stupid power right now, due to budget constrictions, but eventually, I will build a much bigger series 2 or 3, and retune the computer to fit... I would eventually like to see the car around the 400hp mark. Not cheap to do with a 3800, but very easily achieveable, and without having to dig too deep into the stock internals (although that's about as far as you want to push a 3800 without going to better pistons, rods, cam, timing chain, and a very well balanced rotating assembly...
And as for the 1/2 gearing issue, if you're driving it civilized, it shouldn't be really noticeable, and depending on what you go for motor, if you drive it right when you ARE racing, it shouldn't even be an issue because with any decent power and torque, you are better off starting in 2nd gear anyway because the little bit you lose off the line, you should be able to make up for by not having to shift til 50 or 60 MPH...
Like i say, each car is a reflection of it's owner, or at least should be, so it's completely your decision as to what to do and how to build it, and the single biggest thing to do is RESEARCH RESEARCH RESEARCH... find as much info as you can on whatever options you have, and make sure you're as well informed as possible before you make your choice, or start collecting parts, and make sure your ideas will fit within your budget, because it's really easy with projects like these for something small to become a major expense in a hurry...
Other than that, go with what works for you... We have a Club member up here that is quite happy with his series 1 3800SC on the factory 4-spd in his 85 GT that walks all over his neighbor's Z06 Vette, and our Club head just sold his 86 SE/GT after 5 or 6 trouble-free years on a mild 4.9/Izuzu combo. 2 opposite directions, but both were fast cars, both have several years of reliability and mild (or not so mild) abuse, and both are still a blast to drive.
Good luck with your project, and hope to see it on the road soon
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1986 Fiero SE 2.8 Auto - Blackie
1985 Fiero GT 2.8 4-spd - Goldie II - To be driveable this season
1985 Fiero SE Targa - 3.8SC - long term project
1987 Cavalier Z24 2.8 5-spd - daily beaten driver
1993 Bonneville SSEi - 3800SC donor for 85 Targa