So I have made some progress. After talking with Sega a bit I moved my CF Card, Blank Hard Drive, Key Chip, and Video card to another Lindbergh Yellow that I have. I was able to use an external DVD drive and install the game and it reboots / boots up normally. So I took that hardware, moved it back to the original motherboard / power supply / JVS / Sound card and tried booting it and it got stuck at the same spot on the "Now Loading" screen.
So I got a bit curious and plugged a keyboard in, since I noticed that the screen would go blank like clockwork about 20 - 30 minutes after being powered up and sitting and it made me wonder ( also with the fact that you can see GRUB pop up when the game starts loading). The first thing I found is that if I hit any keys on the keyboard that it would bring the "Now Loading" screen back, so then I hit escape and I got a bunch of text which is probably whatever OS they are running going through it's startup. I was able to hold down shift and page up / page down through all the messages and I found a bunch that seem to relate to the IDE bus
They read:
read_intr: status=0x51 { DriveReady SeekComplete Error }
read_intr: error=0x04 { DriveStatusError }
request: I/O error, dev 03:40 (hdb), sector 4
[code]read_intr: status=0x51 { DriveReady SeekComplete Error }
read_intr: error=0x04 { DriveStatusError }
[code]read_intr: status=0x51 { DriveReady SeekComplete Error }
read_intr: error=0x04 { DriveStatusError }
[code]read_intr: status=0x51 { DriveReady SeekComplete Error }
read_intr: error=0x04 { DriveStatusError }
[code]read_intr: status=0x51 { DriveReady SeekComplete Error }
read_intr: error=0x04 { DriveStatusError }
unexpected interrupt, status=0xd0, count=12
reset: success
Then is has what look to be a bunch of normal messages and it halts. If I hit Ctrl-C it spews out a few more pages of these errors and then the white Lindbergh loading screen with the bouncing text shows up, the game loads and is playable.
If I reboot the machine however, it just gets stuck at the "Now Loading" screen again and hangs until I interact with the keyboard.
So today I am going to try and move the power supply over from Let's Go Jungle and see what happens, the next step would be to go into the bios, disable the primary IDE channel and try to connect both the CF card and the hard drive to the secondary channel via a CF adapter. I have already tried a different IDE cable for the hard drive and I think it throws the errors with just the CF card too. Starting to wonder if I have a failing motherboard.