Re: Beat the clock
To some degree it not just the length of the wires, but the differences in length wrt the frequency being used.
I sure hope he's keeping the length of the wires (as appropriate) the same to each (and within) similar functional banks of transistors, otherwise the differing propagation delays will be madness to try to debug. This is normally done at chip layout and PCB layout. Clocking in incorrect bits (on some lines) and not others would surely lead to a long stay at a mental institution.
Slowing down the frequency until it worked might be practical, but with a little attention to the lengths, he might find that he could run at a much higher frequency. Overclock - baby....