Okay, I just tried it on my systems...
I made sure the NEO2 Manager had the 2.9b3 MD menu file (MDBIOS.BIN).
I formatted the Neo2-Pro as N64 with path A2 (the U2 flash) set the the N64 menu file, and path A1 (the Neo2-Pro flash) set to MDBIOS.BIN. The boot path was set for A2 (N64 boots from U2 flash).
I noticed that it didn't seem to write the entire MD menu file, so I went to the Memory tab in the manager and wrote the MDBIOS.BIN file to Menu flash (4Mbits).
I then burned Conker to flash (since it's too big to load from SD), which went fine.
I booted the N64 and ran Conker from flash. I then rebooted and ran Doom from the SD card. All is fine on the N64.
I then transferred the Neo2-Pro to my CDX+MD Myth.
I booted just the Neo2-Pro - it's fine. I then inserted an SD with the 2.9b3 menu on it (same as in flash, but I wanted to see if it boots) and rebooted - it booted fine. I ran a MD and an SMS game... no problem.
So the only things I did different than what I mentioned earlier is to use the latest menu and to burn the MDBIOS.BIN manually after formatting as N64. So give that a whirl.
