So here's how it went. I did what you said, and stripped the system. Nothing but the CPU and the fan and I hooked up the monitor to my onboard graphics. Then I plugged the RAM back in, no problem, and not the CMOS battery. Then I plugged in one hard drive at a time, no problems there. Then I did a quick internet image search and found that the M_Bios LED was supposed to be on anyway. So I plugged in my disk drives. Fine. USB headers. Fine. Graphics card one. Fine. Graphics card two. Beep. Beep. Beep. Beep. Dammit. So I checked the card in another computer, and sure enough. Lots of beeping.
I initially figure is had to do completely with the motherboard because the M_Bios LED hid between my two graphics cards. I only noticed it when the beeping started. Thanks you for the reminder to strip.
Now just to find the warranty card!