I don't want to get hasty and call you a genius yet, but it seems to be working properly. The video files are playing perfect, so I'm going to run it through the gauntlet of stuff that wasn't working previously, and see what reaction I get from the drive.
I just set the BIOS to "Auto" and it was the jumper problem. I had the original, factory HD set to Western Digital jumper settings, but I found out what drive it was, and used the right settings. So now the jumpers are right, and it seems that things are working. And it's also now set to DMA.
The CD drives hooked to the secondary IDE cable were having the same connection problems as the first, with the second disk (my CD drive) not being found...well it's a lot of junk, but the lesson is, as always: I'm an idiot. Woohoo!