Thanks for the reply! After playing a bit more, that's consistent with what I saw. I hooked the 68k up to an FPGA instead of the PC-104 to eliminate the very crude signal timing performance. After doing that, 68k worked fine, even down to a couple Hz. I guess the (relatively) expensive quartz crystals earn their keep.
BTW, after verifying the logic in the FPGA (avoiding tedious wiring of discrete chips), I finally broke down an wired up a version all in discrete logic, with 27256 EEPROM, 6264 SRAM, etc. This FPGA is still in there, but now as a 'chip selected' device for sound, VGA display, PC keyboard input, etc.
68k forever, right??