Might have found an issue that is caused by the HD

Western Digital VelociRaptor WD3000GLFS 300GB is the item.
A western digital raptor 74GB is slaved in for backup storage, BUT here is where I think I have the problem and I don't know why it happened.

I formatted the HD. Installed my Vista, but never disconnected the backup drive with my games/programs that I didn't feel like downloading again. The computer is slow at times, and I am also getting the lowest score for 3DMark06 for my setup. I decided the second harddrive was only to be hooked up when I needed to a: get something off it or b: put something on it.

Since I installed Vista with the secondary hooked up, I cannot remove the drive at all. With either drive disconnected, it only goes as far as asking me to install an OS and that there is none already installed.

Should I reformat yet again, and disconnect that drive?

When you installed the OS, you should have disconnected the slave drive.
If the drive has ever had an OS installed on it before, this can cause the problem.
The old drive has the HAL/ boot sector written to it, and even though the install of Windows itself may on another drive, it will still look to the old drive for the boot sector. When you did the new install of Windows, it will update the boot sector on the old drive and keep using it even though the software is installed on another drive.
Rule #1 about installing an OS to a new drive. Unplug all other drives except the DVD/CD drive and the hard drive you are installing the OS on.