The dimensions I came up with are 7.5" wide by 4" high by 8.25" deep (from the back to the dash kit). I made the enclosure 6.75" deep to leave room for the LCD. I probably ended up with about 1/4" to spare. But I did not disassemble the LCD. I'm guessing you could save a bit more room if you did. I should have made my enclosure slightly deeper, since my motherboard is pretty snug (it's touching the sides).
Regarding the amp, yes there are four inputs...each tied to a single output. I read on the 41Hz.com forums that it was perfectly save to tie inputs together to make it a two-channel amp. I'm simply connecting to the stereo output from the PC to into the two channels. Of course, there's no front/back fade now...but it's a small car, so I don't care. I'm connecting the amp to the stock speakers, so it's using whatever crossover Honda installed.