For the suspected BIOS mess-up, look in your MOBO manual and use the jumper to reset your BIOs to it's virgin state. This is done with the power off! Just find the correct jumper, move it to the reset location, count to five and put it back to the original position. Then go back in and rest your BIOS Setting to what you need. For help on the correct settings I have included a couple of Links.
For the IDE Bus settings, use the Hard drive on the Primary IDE (IDE1) with the jumper set to master. And the DVD on the Secondary IDE (IDE2) with it's jumper set to master. If you have other devices attached to the IDE buses set them to slave.
Another item, since you built this computer, did you install the motherboard drivers. You didn't tell us what bord or CPU Brand you were using. Intel CPUS with Intel chipsets do not need the drivers, but Via Chipsets will have to have the drivers installed for the IDE Buses to work properly.
http://www.lostcircuits.com/index.html
http://www.rojakpot.com/Speed_Demonz...uide_Index.htm