If you're getting to Windows, sounds like the jumpers are okay.
One way to check is in the BIOS. When your PC first powers on, you should see a screen that says to push F1 or F2 or DEL to go into the BIOS. You should then be able to see if your new HDD (hard drive) is being recognized.
Although, when you talk about your display being messed up, and other things going wrong, it could be a corrput registry that's causing that.
Have you tried just unplugging the new drive to see if it goes back to the way it was before?
Your mobo is your motherboard btw.