Do not connect the 100GB HDD via USB. G3 iBooks have USB 1.1, you need to move up to a G4 iBook to get USB 2.0 and even then USB 2.0 is slow. Just replace the original HDD and use that bus. Sooooooo much faster that way.
Oh, and you do have that FireWire port at your disposal.

wrt issue 2, isn't the iBook's drive ATAPI as well? (just like the iMac's if you remove the adapter board)
As far as I have seen, a Lime iMac would be a tray loader, and they use normal slim PC ATAPI drives, just like the Lombard/Pismo(at least my TL iMac and Lombard use the same connector and can take PC ATAPI drives(I have tried it in both and people have written elsewhere about it)). I also recall hearing that you could use some iBook drives in the Lombard/Pismo so they must all have the same connector.