William,
I think I understand your description. Ryan is correct in that most amps operate best, thermally, if the fins are oriented vertically. That said, I very much doubt you would have a problem in your design, given that the fins are still above the output devices and in open air. I doubt the woofer air movement will be a noticeable advantage, but certainly can't hurt. In my experience, plate amps (at least on commercial subwoofers) do not get very warm at all. In fact, one I built just last week, after quite some time of driving it near reference levels, is barely warm, and I do mean barely. Now this is only a 125w @ 4 ohms amp (and that's the impedance woofer I was using), so it may be that the 250w+ amps common these days, run a lot hotter.
I agree that 4" should be enough for the small cabling and limited access. After all, unless you are constantly tweaking and testing, how many people actually touch their plate amps? Unless your front end equipment is in the stone age (by that I mean > 5 years old

), you won't need the crossover, nor the level control, and how many people are constantly fiddling with the phase switch, honestly? I have zero controls on my subwoofer amp and I don't wish I had any.
Aaron Gilbert