Just an update, since some of you have been very helpful-
I got the new motherboard in. I hooked it up, added my RAM, attached the hard drive kit I bought off of someone on KLOV, plugged in the serial ELO touchscreen I have, crossed my fingers, and switched it on. It booted up just fine, so I must have had a bad motherboard, IO card, or riser card. However, I have two more issues I need to resolve:
1. The hard drive boots up just fine, but the serial touchscreen doesn't seem to be recognized. Now, I hadn't tested the serial functionality yet (got the touchscreen late last week), but I have no reason to think it shouldn't work. I brought it with me to work and will test it out soon.
2. Like I said, it does boot, but once I am in, I get these weird graphical glitches sporatically on the screen. It looks like lines/shifting across the screen. Should I pull chips on the board and clean them? The board is very, very clean compared to my original mobo, but I've read that some of you have fixed glitches on arcade PCBs by pulling and cleaning chips.
I feel like I made progress so far, but there's still more to go!