Listen, you only run the Builder when the "virgin" drive is connected. If only the virgin drive is plugged in, it would be the Master and would not be jumped as Slave.

It sounds like you had both drives plugged in when you ran the builder which is a big NO NO in the Upgrade Guide (and has a very big warning about this). If the virgin drive was the only thing connected, and you had it jumpered as Slave when you ran the Builder, it would not have worked. If it didn't work, the virgin drive would never have been formatted and would explain why emplode does not see the extra space (but the drive would still show up as a physical device during the boot sequence).

Listen, even if you did that correctly, you'll need to install the Developer version of the 2.00 software here.

Listen, if I were you, I'd read the Upgrade Guide first, from beginning to end. And then start over from scratch and take you time.