I can't get an a: prompt with the floppy. Only when I boot from the CD and use CD support. I thought originally it might be a floppy drive or controller issue, but it lets me boot with another drive installed.
Earlier I booted from the CD to get an a: prompt. Then I ran the wd diags directly from the prompt. Now I get an error code. It was 0104, which according to the WD site means the drive is not ready. That would mean something with the connection in a normal situation which this is not. I called WD and they said the same thing until I told them I get the same I/O disk error when I put the drive into another machine. The tech immediately said it needs replacing.
I think at this point it is best to start off with a new drive. Having a brand new built system for 2 months that I can't even enjoy yet is getting tiring and frustrating. If I still have probs with the new drive than there is a good possibility that it is a second bad mobo. While I am waiting I am going to update the bios on the mobo as well.
I would like to thank each and every one who contributed advice in this thread. You all have been very helpful even though the prob was not resolved. If when I get the new drive I still have problems, I know where to go. In the meantime I think I have a look around the rest of the forums.
Thanks again everyone.