Frequent BSOD, not sure why

This past summer, I rebuilt my desktop with almost all new parts except for the hard drives. One of my hard drives appeared to have died, however, so I had to replace it. I had a lot of trouble reformatting them (I was unable to do so in the Win7 installation) and ended up having to do it in Linux Ubuntu on a CD. Eventually, I was able to format both drives, and got things working. I now have Windows 7 running fine, but for some reason I get BSOD about 5 times a day. Another strange thing I've noticed is that any Windows loading screens (for instance, asking if I want to boot in Safe Mode, etc), I cannot control them with my keyboard. It works fine in my system BIOS, but does register for menus such as this. Sometimes it works fine, but every time I get BSOD and it restarts, I have to simply wait for the countdown to auto-choose to boot normally. I thought that my older hard drive (dead, but still hooked up) might be interfering with things with old motherboard drivers on it, so I disconnected it. However, for some reason when I disconnect this hard drive, my computer will not boot Win7. The drive does not show up in BIOS or Win7, but is required for me to boot at all. Any idea where to start to try and track down this issue? Thanks.