Fixed!

6V was apparently the magic number. I soldered a second AAA holder in series with the first, then added the 2 extra batteries and tested the voltage, got 5.2V, so I replace the original 2 batteries and got a 5.9V.

Ran the same clock test as before and this time it incremented the clock just fine.

Sweet, now I think this board is 100% functional, and is pretty darn quick. All I need is the memory I ordered to up the RAM to 64Mb and I'll be done.

Thanks for the help!