I found a problem with my LD-V1000 AVR code; I was putting the AVR into input mode (with 0xFF pull-up resistors enabled) right before disabling the status strobe.
This caused problems with Super Don because it uses LS374 IC's (positive-edge triggered flip flops) to store the LD-V1000's status and this value is stored when the status strobe ends. So by putting the AVR into input mode and enabling the pull-up resistors before ending the status strobe, the AVR was causing the LS374 to store a random value close to 0xFF; usually it would be 0xF6, but it was always somewhere between 0xF0-0xFF.
So I just changed the AVR code so that it ended the status strobe before going into input mode and this seems to have fixed the issue Warren was seeing with Super Don. He says that it is now locking up later so that's the next thing to troubleshoot. But good progress being made!