Took my HD2 apart. I found there is very little air space between SoC and shield. I put some heatsink grease on the SoC, put the shield back on a took it off, and saw grease on the shield so it looks like they are almost touching. I put some grease on top of the shield and only a little bit got on the LCD chassis, so they are almost touching, but not quite. I saw on eBay the silicone thermal pads come in 0.2mm and 0.5mm thickness, which might work between the shield and LCD chassis.
I did notice just with the heatsink grease between SoC and shield, and a little grease between shield and LCD chassis (though with rather poor contact), I can now play Fruit Ninja without any pausing or slow-down! It's never been like that before, so it seems my idea really worked. Might work even better if I'd used a silpad between shield and LCD chassis.
Sadly, when pulling the motherboard, I may have damaged the camera flex cable. My camera no longer works. Also, the flashlight works with delay and only through the Torch app that came with Tytung's CM10.1. I used to use Nexus One Flashlight widget, but it no longer works. Torch works, but is delayed. Volume works fine though. Thinking it might be a bad connection, I removed and reinstalled the flex, but same problem. Does this sound like a flex cable problem? I saw I can buy a new flex for $13 on eBay, but I'm not sure it's worth the cost, effort, and possible gamble because maybe it's not the flex.