Wow, you did make a bunch of changes. Looks damn good. I like the idea of the spare holes for decoupling.
I played with it a bit, to see if the digital lines could be unkinked any. I swapped the functions of J5 and J6 and switched around which pin goes to which parallel port bit. The only thing that might cause a problem (if you're not writing your own software) is the way I switched a couple pins from the 'control' output byte. Easy enought to switch 'em back...
While I was playing I also removes a redundant power trace, ran grounds to U1 and U2, and switched around which output of U2 went to which ADC input.
I got a little carried away, but I really like puzzles.
