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Is this totally screwed up? Should I maybe have my main HDD and DVD burner on the same IDE channel?

Well, the two considerations are (a) two devices on the same channel have to take turns using it, and (b) sometimes (perhaps only on Windows?) if you mix device speeds on one channel, it goes at the slower speed even when talking to the faster device. So if you often use a lot of bandwidth to both your primary master and primary slave simultaneously, you might improve things by moving them to separate channels. But if your DVD drive doesn't understand Ultra133 (or whatever the speed of your primary master is) then you shouldn't do that, because it might destroy the performance of whatever it shares a channel with.

Peter