Ok, so I have used the 3rrod x clamp fix successfully on previous xbox 360's but the one I am working on now started off with a different Error code (E18) than the usual 3rrod consoles normally have, that I've had. After a couple tries, the X-clamp mod works and I am able to run the console but after 5 minutes the screen freezes.

I can do any mod to fix the problem, fans in front of the heatsink(s) etc but I don't know what would cause the freezing. My thought would be the GPU is too hot but the CPU isn't. Am I close?

And more information on this console:
When I cracked it open it was filled with dust, none of my consoles had this much dust and after taking the board out, there were spiders under it! how could spiders have gotten in there lol
I guess the person had it in an enclosed area for a long time, could explain the 3rrod.

After I took the heatsinks off there was almost no thermal paste left, could it have burned away?? I don't know but I guess I won't be disappointed if I don't fix it.

I'm 100% sure that its freezing because the CPU heatsink is not making enough contact to the chip dye because you said the cpu doesn't get hot. Only the CPU has a thermal sensor so that's why it shut off to know it was going to overheat. The GPU doesn't have a thermal sensor so will overheat and melt, this is the cause of the RROD in my oppinion, that and the fact they didnt use 2x 80mm fans to run the xbox to begin with.

I xclamped a box that just froze but never gave errors, took me 30 mins to get it to stop freezing with xclamp because the heatsink was being heald on the cpu wrong, you need to put it down evenly on all sides. I applied thermal paste like 4 times to get it right. Some people sand thier heatsinks on the bottom to be shiny and heat conductive.

Well thanks, you're right it's the cpu, I didn't bother to redo the xclamp mod,
I added two 40mm fans to both sides to the cpu heatsink blowing air one direction out of the heatsink and it no longer freezes

Doesn't that mean that the heatsink IS making enough contact to the cpu? The heatsink just isn't enough, I guess, even though it's the new model heatsink.
Oh well problem resolved
It is weird, though, that the cpu overheating wasn't causing the 2 red lights like it usually does, for me anyway.

Edit: Oh I was just guessing that the cpu wasn't getting hot enough to cause the freezing because I didn't know the cpu could cause it I thought that kind of problem would lie in the GPU. but yeah it seems the CPU heatsink gets extremely hot and I don't know why. So yeah the fans seem to do the trick! All they're doing is removing heat from the heatsink.

If the CPU heatsink is getting extremely hot THAT IS GOOD as long as you move air through it. It's doing its job to remove heat from the CPU! Instead of circulating hot air around your case, consider taking 2 or 3 80mm fans and attaching them to the right side of the console pushing hot air in, without the right plastic shell on, that's what I do and it lowers temps 10-20 degrees and it never reaches 140. A good idea would be to cut a hole in the top of the shell and put a 70mm fan there, you can fit a 70mm fan between the ROL's wall and the CPU, or you can put any size fan externally of the shell with a hole in the shell.

Just my 2 cents, You should really redo the Xclamps.

Its sounds like the Heatsink is barely touching the CPU.
After an hour or so of playing problems may come back.
You added more fans but your really just masking the real problem.
The CPU shouldnt heat up enough to cause frezing unless the Heatsink isnt properly seated on it. Which im guessing is the case.

EDit: if the heatsink is getting real hot than disreguard my post.