Any computer parts vendor should have a selection of thermal pads to choose from. NewEgg surprisingly doesn't.
http://www.amazon.com/Cool-Silver-Pad-Overclocking-performance/dp/B002VM7GO8/ref=sr_1_2?ie=UTF8&s=electronics&qid=1266766026&sr=1-2
It would be kind of a kick if a failed EE could result in a YLoD though.
The disassembly/reassembly process shouldn't take 4-5 hours after you've done it before since you should be familiar with the process. It takes me about 5-10 minutes to strip a PS3 down to the bare motherboard if I rush (there are fewer parts for the 40GB SKU). The longest part of a repair should be waiting for the board to cool down before moving it.