Shutdown temps need to reach 80c or 85c I think before the CPU will physically turn itself off. A short duration without a HSF shouldn't fry your E6300. The internal thermal protection would kick in before that happened. The only thing you could have done was damage your HSF or your fingers by removing it so many times. Seriously though, the push-pins on those stock HSF's wear out with excessive removals. Also, I assume you removed the HSF while having the motherboard still in place in the case? That's a bad idea really. With the push-pin type HSF's you should really remove the motherboard and then install it so you can verify that the little black pins have gone all the way down (you will see the tips sticking out from the flipside of the board). The only HSF's you can safely reinstall while the motherboard is still in place is the ones with clips and/or that screw down to a backplate.
that was just hot enough to clock throttle not shut down.... nothing has been hurt. My friend ran his P4 throttling like a bastard for at least a month @ 102c(solid dust heatsink) wondered why it was soooo laggy ....
Well, I agree with everyone else that you most likely didn't damage your CPU. You could do a test with prime95 for 24 hours to verify that if you wish.
There is 1 thing that nobody mentioned, and was a big red flag when I read your post and before I scrolled down to read the responses.
Why did you remove your heatsink to clean it?
The more you remove/reinstall your heatsink the more likely to damage the heat transfer surface that is so important. I can't for the life of me understand why ANYONE removes their heatsink unless they're upgrading or troubleshooting/repairing. Heatsinks are one of those things you install once and don't mess with until you HAVE to. I use the analogy of "Would you pull your car engine out of your car because it was dirty?"
I need a damn good reason to do ANYTHING to my CPU/heatsink before i touch it. I clean it fully installed with a can of compressed air. If it's really dirty I take the computer outside on the porch. But I see no reason to EVER remove the heatsink aside from the 2 reasons I mentioned above. The AS5(or whatever you use) is designed to fill in gaps that are measured in microns. If you can see a scratch, you are WAY past microns.
When I build a new rig and I sell the old, I sell the old as a CPU/motherboard/RAM combination. I keep everything installed and give it to my buddy FULLY assembled. I tell him that I used AS5 and it is installed according to the AS instructions, and they never remove the heatsink and reapply. AS doesn't break down, and more than likely by the time you actually care about AS not performing at 'full capacity' you've replaced it anyway. I think the time to breakdown AS was something like 15 years. I'm not sure I'd keep a computer for 1/2 of that.
I'm sorry if it sounds like I'm trying to beat you to death, but I see people constantly post about removing their heatsink to 'check' to see if it's installed properly, then reinstalling it when they see it was done correctly. If you remove it, you are supposed to go through the whole reinstallation process again with a clean(yes, clean) surface. The bottom line is you CAN'T verify if you did it right or not. You can only go by your indications. You have to rely on your temperature indication to tell you if you did it right or not.