I'm not quite getting this detail from your post: do you have one of the drives plugged in via USB? The external USB ports on that machine are v1 and are extremely slow. Another fishing expedition: do you have the drive(s) journaled? That could also slow things down. I had a G4 tower for many moons. It just wouldn't quit!

20" iMac, 2.4 GHz 2G/500G, Canon MX850, Airport Extreme, Airport Express w/Audio, Bamboo Fun tablet; 13" Macbook