The kicker is, I want to do this without having to take all my music off and back on to the unit.

The drive upgrade guide has specific instructions on how to handle this. Have a careful read through the drive upgrade guide and you'll see where it's covered.

Could I get away with building the 40 then copying the FIDs across from the 20. Reattaching the old 40 and rebuilding the database?

That's essentially what you'd end up doing, yes. It's all covered in the upgrade guide.

And to answer your question about which one is which... The primary and secondary drives are determined by jumpers on the drives themselves, not by their position on the cable. So whichever one has the jumper is the secondary drive.