Since you are planning of leaving them stock I would go with the 390. If you were building an engine using aftermarket parts I would go with whatever you had or was available. If you look around a bit parts availablity won't be a problem for the 390 and the low power/torque of the 400 is easy to overcome with compresion, cam, intakes, etc. I have had several of both engines and never had any major problems with either one.
David.

 

If your looking to throw in a stock engine, 390 more power, less smog. If you want to build up a engine, 400, you can't beat 4 inches of stroke for low end. I'm just getting finished with my 400, around 450 ft-lb, 350 hp. I hope my Trailer Special radiator will be enough!

 

if theyre original all of my trucks still had an emissions sticker on the drivers side valve cover and say the engine size, hopefully one still has that....my 360 said 360 my 460 said 460 and my 351M said 400/351M(so im not really sure what that one really was since all i did was scrap it for parts)
i would be convinced if the vin matches and has a four barrel intake( and looks to be stock) i would be confident that its a 390, even if it becomes to be a 360 i love mine and it has great hauling power.
ive never had a 400 but the 351M's ive had to deal with didnt make me happy.
from looking thru catalogs there seems to be much more available for FE engines now days than 351m/400, plus, like said before they didnt make those engine but for a couple few years. i come across a lot more vehicles with FEs than M's maybe thats just me
I say choose the truck thats looks best taken care of and go with a manual trans hopefully

 

The short lived history of the 335 class engine (351C, 400, and then the 351M) can be attributed to a number of things. The 351C was a great engine, no bones about it. From what I understand, Ford wanted to build on that platform for the larger cars that were coming out at the time, and also for the truck market. As a result, they designed a taller deck 351C, which emerged as the 400. That would seem a good idea on behalf of Ford, but the economic picture then had a major effect. If the 400 could have continued to be developed without any external influences, I think that its potential could have been realized more fully. Since this was the mid-70's, however, the fuel crunch became a major influencing factor on the direction this engine would take.

Ford would reduce the compression, retard the timing, and basically clamp down on the capabilities of this engine so as to attempt to comply with the newly founded emissions laws that were beginning to rear their ugly heads at the time. The 400 ended up being a pale shadow of what it could have been, if those influences weren't at issue. Ford even went so far as to destroke the 400, and produced the 351M as a result in an attempt to further comply with the regulatory requirements, and the economic necessity of the time. And yes, the 351M is merely a short stroked 400, which is why there is absolutely no visual differences between these two engines (the differences are internal....crank and rods).

I believe that if the 400 was developed earlier in history, or if the fuel crunch of the 70's had not occurred, the history of this engine would have been completely different than the few years it spent in existence. The simple way to recognize this possibility is to ask a simple question: If Ford had no original intention of exploring what this engine could do, they why did they give it the longest stroke of any engine they ever produced? I think they did want to explore it, but the circumstances of the times precluded them from doing so, and the 335 class engine (with the exception of the 351C) faded off into mediocrity.

I suppose this is partially why weirdos like me kept the 400 instead of going to the 460, or other engines, as I wanted to try to keep to some degree, with what came in my truck. Granted, I lost my mind and spent waaaaaaaaaaaaaay too much money, but I ended up with a 400 based engine that will do the job quite well. Besides, I like taking the path less traveled......and I like that confused look from guys that look at my engine and realize it's in the 335 engine family.

This rant really isn't about arguing with people about what engine is better, but moreso to attempt to illustrate why the 335 engine family may not have existed as long as it could have. I still say the 390 is an excellent engine, and if I had to choose between a 390 and a 400 in purely stock form, I'd take the 390 every time. BUT....if I were allowed to make a few modifications without going off the deep end, I'd consider the 400 strongly. Just my $0.02

 

It sounds like it boils down to which truck I can get the best deal on. Thanks for everyone's input.

 

The old Fe is a workhorse, and can take alot of punishment, stock or modified, in whatever cubic inch.
The 351M/400 has a bad rap due to emission bandaids of their era. Yes the 351C paved their way. Stock production block, albeit with mods, cleaned up in enginemasters competition! All I hear is crickets about the 400 chev and dodge engines in those respects, for actual, similar stock bottom ends. Just too bad the competition doesn't have the best configuration of valve angles, flow etc.

Like any good well thought out project, Research!
chronological order of engines I have dealt with, 351C-2V, 460-4V, 302-2V, 302 EFI, 302-2V, and 5.0 HO Mass-air-efi, 429-4V, 360-2V, 390-4V, and back to the 429-4V.
Problems; water pump, fuel pump, starter, radiator, alternator=minor wear parts.
Ford engines kick ***!

Be prepared when getting/ordering parts, not all parts guys are smart like Numberdummy! They seem to be familiar with chevy stuff, and nowadays it will be import crap.
Know your parts, your mods, and how to get what you want.