The biggest difference between a 400 sbc and other sbcs is the fact that the 400 is externally balanced. That means that you have to use the 400's flexplate/flywheel and harmonic balancer. Other than that they are externaly identical.
Internally, the only difference (other than bore and stroke) is the presence of steam holes in the cylinder heads. The reason 400s got a bad rep for overheating is that the early hotrodders (well, early in the sense of bein the first ones to try 400s) would slap their double-hump heads on and run the heck outta the motors...and yes, they would overheat. They didn't realize that they needed the steam holes drilled in the heads. Now if you get performance heads, specify that they're for a 400 and you get "holes in your head."
I run a couple of 400 motors. One in my 80 El Camino and one in my 85 Monte SS. They're great motors. I have another one sittin in pieces in the garage, just waitin for the next project.
So no, I wouldn't let the little differences steer you away from on at all. I think you'll really enjoy the torque you'll get from it. I remember when I first put the 406 (.030 overbore) in my 85 Monte Carlo. It turned it into what I felt an "SS" should have been all along. Now it's bein redone (incarnation II of the 406) to run on the salt flats.
hth,
