Hi Jeff, I went back and read your configuration again to make sure I understand it. First go read some tech information and jumper settings on the WD site here
it will tell you more than I ever could. I don't think you should have a problem installing a second disk in a 2 year old system. It would may work out better using cable select instead of master slave jumpers because the position of the connectors on the cable will determine who is who.
I experienced the same problem of plugging the disk master(only one disk on the cable) and it would not work. After much research and email to WD the solution was to plug it either cable select or remove the jumber achieving the same thing.
A suggestion, maybe you have the master disk on the wrong connector, as connector position determines master or slave. So you can see how jumper and cable position may confuse the issue. But please go to the WD site and read their stuff its very good. They also have a diagnostic program you can down load to help out.
I hope this information helps.