The kicker is, I want to do this without having to take all my music off and back on to the unit. Also, the 20 is the main drive. Could I get away with building the 40 then copying the FIDs across from the 20. Reattaching the old 40 and rebuilding the database?

Yes, that should work. I did it this way when I replaced both my 30gigs with one 80gig. Just be sure that the disk builder does it's job correctly. Sometimes it doesn't create all the necessary partitions. This can be solved by running the disk builder a second and maybe even third time on the same disk. The be sure it's OK, I would recommend building the disk 3 times.

The slave disk is indeed normally the one on the left, but it doesn't have to be. It's easier to identify the slave drive by looking if it has a jumper on it : the master disk does not have a jumper.