Limit usage of 1 core?

4th solution: Install a better Heat Sink and fan assembly.

Get your self one of these.

http://www.newegg.com/Product/Product.aspx?Item=N82E168...

What we need to know is how hot each of the cores is getting because it could be a power supply issue, instead of a heat issue. Power supplies get less efficient at high temps and thereby can supply less power. Not enough power causes immediate shutdowns, but CPU overheating usually just throttles itself.

So, what PSU do you have, what are the rest of your specs, and how hot are the cores at 100% load (ideally on your hot day).

Open up your task manager and go to the processes tab. Find 3ds max in that list and set affinity to use only 3 of your 4 cores. Than the program won't touch your 4th core and you won't need to down clock or anything else.

I actually have a Cooler Master Hyper TX2 currently installed. I know it's not that good compared to higher end solutions, but it was actually the best I could find and when I bought a cooler. I'm looking around for a better cooler now, but I need a temporary solution for those hot days when I have to render.

My temps at 100% load are 72 69 66 65 (tjmax 100) on regular days. I know that's dangerously hot, but I can't seem to get it any lower. I've seen the hottest core hit 76C on hotter days which would have an ambient temperature of around 37 to 38C. That's when it shuts down.

Specs:
PSU: Antec Neo HE 430.
GPU: 8800GT 512mb
CPU: Q6600
RAM: 4GB (2 sticks)
Hard drive: forgot the model, but it's a 320GB Western Digital drive

So at the moment I'm just trying to find a way to throttle the hottest core without compromising the speed of the others if that is even possible. Or am I, at the moment, stuck with slowing the whole thing down?

Dekasav makes a VERY good point; an overheating CPU should throttle, not shut down. While I am an Antec fan today, I definitely wasn't some five years ago; I'm not sure your old HE 430 is up to the job [any more], even though it ought to be enough for your rig. If only because of its age, you might consider replacing it. An Earthwatts 500W PSU would settle any question of the PSU being enough.
Do you have decent airflow through your case? Airflow isn't just a matter of lots of fans, it's a matter of having whatever fans you have working together to create a current of air through your case. Usually, front and side fans are intake, and rear (including the PSU) and top fans are exhaust. Is the PSU fan running? If you have more than one fan, is at least one of them an intake? If not, the PSU fan may be struggling against multiple other exhaust fans, and not be enough to keep the PSU cool. Check out those things and let us know.

Well, assuming the older B3 stepping for your CPU, and running it flat out, the PSU sizing calculator at http://www.extreme.outervision.com/PSUEngine is still showing only 402W with 50% capacitor aging. Still could be heat though. Let us know what fans are in your case, and what direction they are blowing. Have you blown the dust out of your case within the past few months, and out of your fans and the fins of your Hyper TX2? You may need to remove that HSF, clean off the old, hardened thermal paste, reapply a new layer of something good like Arctic Silver AS5, then remount the HSF.

I have a front intake, a side intake and a rear exhaust. I'm pretty sure it's the heat causing the shutdown though since that's what it did when my hsf wasn't properly seated and my temps hit 80C idle.

I've looked around some more and I can't find any mention of slowing down a single core. So I guess I'm stuck slowing down my cpu until I can find better cooling.

That's the usual arrangement for fans. Maybe your HSF is still not seated well; the Hyper TX2 is a pretty good cooler (reviews are at www.frostytech.com). Is the PSU fan running? It seems more likely to me that it is your PSU overheating, not the CPU, as the latter will throttle itself, but a PSU will simply shut down.