Everyone is right, there is no issues with 7200rpm drives in eMacs. They are prone to unfathomable jumper issues however. Check the jumper settings on the old (OEM) drives and if possible one of the optical drives. If the old HDs are set to cable select, then it might be worth changing them to a master/slave configuration. I'm not sure which way around works best, you may have to try both. I know they are a pain to rebuild but sometimes its the only way, and once you have worked it out you won't have to work it out again.
Since they work in target mode for you to install onto, what Mac are you installing from? If you are using a Leopard image from an Intel Mac its not going to work. You need to do it from a PPC unit.