This is a really cool motherboard, but is extremely finicky when it comes to hardware and software compatibility. I think I finally have this 99% solved and just wanted to share what I have found out.

Intermittent parity errors:
I first thought this was a memory issue, but all the ram chips checked out in my Retro Chip Tester Pro. This turned out to come from three add-on cards. A Juko M16 multi I/O, Blue Lava XTIDE and Lo-Tech EMS. I replaced the Juko M16 for a MT-881 multi I/O card. I replaced the Blue Lava XTIDE with a Monotech XTIDE card now running in Hispeed Mode vs legacy mode. I removed the Lo-Tech EMS adapter and just use the 320K available on the motherboard as EMS memory. The Lo-Tech EMS board would fail running EMSTEST during the I/O disk test. Now that I have replaced all 3 cards, the parity errors have stopped.

Issues running adapter cards with 1 WS vs 3 WS:
Not all adapter cards will work with 1 WS enabled. The RTC on a Everex EV170 and PicoGUS are two examples. I use a RTC8088 for a RTC card a RadLib from TexElec for a sound card. Depending on the adapter card your mileage may vary.

Applications hanging on exit:
This has happened running Turbo Pascal 6.x, Turbo Pascal 7.x, the Microsoft Editor among others. I traced this down to using the Cute Mouse v1.9 driver. I have since switched to the Microsoft Mouse v6.24 driver and this issue has disappeared.

Applications hanging on starting:
Paku and Landmark 6.0 both have this behavior. Paku was fixed by just switching to 7.16MHz and Landmark 6.0 by switching to 4.77MHz using the CONTROL speed switching utility in a batch file.

Intel CHKCOP 2.20 & MCPDIAG hanging during testing the 8087:
The 8087 will hang about 4 minutes into the test. Using Intel CHKCOP 2.0 eliminates this issue and every other FPU diagnostic I have tried works fine. I have run several FPU intensive applications for over 5 minutes with no issue as well. I am just going to attribute this to some kind of software glitch.

Final thoughts:
If this was not such a rare motherboard, I would have never spent the amount of time and effort to work through all these issues. In the end it was all worth it!