Video Card overheated, but something else must've gone wrong too. Need advice.

I had a video card overheat on me at the beginning of this week. I replaced it tonight, and did a quick cleaning of my computer. I have built a bunch in the past so I'm fairly certain everything was set up correctly. I powered it on and I got a boot error, it was trying to boot from the CDRom so I went into BIOS and tried to set it to my hard drive. It wasn't able to find it. I have two hard drives, and neither showed up. So I went to the basics, I unplugged everything except my main hard drive. It found it, ran a bit slow but found it and it allowed me to boot. So then I shut it down, plugged in the CD Rom and started it up. It booted fine again. Everytime I connect the second Hard drive it is only finding the CD Rom and Floppy Drive. Everytime I disconnect it, it recognizes the primary harddrive. I have them set to master and slave, nothing has changed I just unplugged everything, cleaned it and plugged it all back in.

Does anyone know what may be happening? I am completely baffled. I will probably take the hard drive to work tomorrow to see if the computers there recognize it.