Mclovin, I tried running the CHD file I have under Mame and it worked flawlessly. I'm thinking the CHD is good at this point if green and red boards have the same software. Next I tried disconnecting the drive and the system gives a count down trying to detect the drive. I read on another board to try a cd-rom drive in the other IDE port, which was detected, but still the same error trying to read data from the hard drive. I also checked the voltage out of the PSU and it read 5.10v during boot up of the hard drive, in-case I was losing voltage while it spun up. No luck there either, PSU, hard drive and software are all looking fairly good.
Lilshawn, I'll take the IC's out and clean them up to ensure they're good. Would either of you know how to test the IC's to see if they're functioning properly? Holding the start button takes me to the system tests, and everything checks out except the hard drive test from that menu.