I assume you are saying that the processor is located in a different spot on the logic board (so the heatsink is as well)...is there enough room to buy an aftermarket heat sink and cut it to fit? These are readily available at computer shops and pretty cheap. I'd also look into installing a fan while you have it open. The iMac DV was designed to cool itself through the natural movement of hot air upwards (convection maybe?). However, on my brother's 500 mhz DV iMac I noticed it gets fairly hot. A quiet slow moving fan would probably do wonders.

Combine your new logic board with a fan, larger heat sink, and overclock it here.

You would have a badass iMac laugh

PS. Can you take pics of the logic boards so we can see the difference you are talking about