I don't think you gave us quite enough information. How were your drives connected before and after? Obviously, you have another hard drive, or you wouldn't be able to be ripping. So you previously had a hard drive, the Plextor, and an optical drive. Were they hooked up with the hard drive as a single on the primary chain and the Plextor and the optical on the secondary chain? And now you've got a new hard drive, which is set as a primary, so now it's the hard drive and the Plextor on the primary chain and the new hard drive and the optical drive on the secondary? If this is the case, then the fact that the device that's on the same chain as the optical drive wasn't and isn't working properly points a finger at the optical drive. Try removing it from the situation altogether and see if things improve. You might also try changing it back to the original configuration and see if it's slow, then remove the optical drive and see if it speeds up. It might be that the optical drive is broken, horking the whole chain, or it might be disabling DMA for the whole chain, or something like that. If Mark Lord was around, he'd probably be able to give you some more information.
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Bitt Faulk