Ok, I finally got around doing all the mods I wanted to my T60. The difference in usability is night and day. I can't believe how big of a difference you can make to this laptop, if you spend your time on it.
My aim was to make it a lot more quiet and cool, but without sacrificing any performance. I am happy to say that I managed to achieve my goal, thanks to this thread and after some google research.
Here are the specs of my system: Thinkpad T60 15 inch, FlexView 1400 x 1050, Ati x1400 128mb, Intel Core 2 Duo T7600 2.33 ghz, 3gb ram, Kingston V300 240 gb SSD, Intel N 6200 Wifi card (no whitelist BIOS, so that this card works).
I swapped the original heatsink assembly out with a Thinkpad t500 heatsink (the one with double pipes for the cpu, not sure about exact part number). This new heatsink is definitely a tight fit between the ati gpu and keyboard bottom plate, but it fits, and the good news is, it can transfer heat from the gpu to the steel bottom plate of the keyboard. I also added copper shims between the heasink and keyboard bottom plate on the cpu, and at the other end of the heatsink, close to the top left corner of the keyboard, where it exhausts the heat. I used Arctic silver MX4 paste everywhere where contact is being made and heattransfer is necessary.
I also removed the heatpads from the heatsink, and used the same type of copper shims (15mm x 15mm x 0.8 mm) as I used everywhere else, using more where it needed, like on the North bridge (?) that is under the gpu at the very end of the heatsink pipe, using thin layers of MX4 paste between the shims. One thing I was afraid of was cracking the Ati gpu die, as it's very tight there, and removing the heatpad, the solid copper block makes contact with it, and the keyboard also slightly pushes the heatsink assembly down on it. But luckily no issues, and I really don't think there will be problems with this setup. Although it would be definitely risky starting to smash the keyboard in anger. Luckily I am a very calm guy

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Then I installed tpfancontrol (a Thinkpad fan control program), but I didn't really tinker with it (you can change temperature treshold values etc.), left it on smart mode, edited the TPfancontrol.ini file so that on system startup it will stay hidden (the temperature monitoring window). The normal treshold is 65 celsius, under that the fan stays off, 65 and above the fan kicks in, first on level 1, then ramps up as temps rise. Level 7 is the max. As you will see after all the mods, it will never need to go higher than level 3.
After all this I needed to find a program that I can use to undervolt my CPU on Windows 8.1 64 bit. RMclock doesn't work, but after lots of searching around, I found a program called CPUgenie, that does just wnat I need. It's not free, after the demo version it costs $15, but I think it well worth it.
CPUgenie has an automatic voltage adjusting and testing function. I run the short version of that test, ~3 minutes per voltage, it goes through on all the frequencies starting from 1000 mhz all the way up to 2333 mhz, gradually decreasing the voltage on each frequency level, and setting the lowest safe values. During this test I had two bsod-s (blue screen of deaths), furtunately the program is intelligent enough, and when the sytem restarts and you launch CPUgenie again, it detects that bsod occured due to too low voltage, and offers you the option to set the last tested safe voltage value, and continue the remaining of the test from there.
It really saves time, unfortunately this method is still not perfect, at least not the short 3 minute stress tests, as after finishing with all the tests and setting the new lower voltages, I still had a bsod when tried to open Youtube, so I added one extra voltage value manually to most set values, just to be safe. Then I run Pime95, Unigine Valley, and did multiple other things, the system is rock solid now.
Just for your interest here are the values I ended up with, keep in mind these values change from cpu to cpu, so even if you have the same cpu and computer, you need to do your own stress tests, you can't just copy these values, but I thought I can give you an idea that what is achievable:
Frequency factory voltage new voltage
1000 MHz 0.950 V 0.950 V
1333 MHz 1.000 V 0.950 V
1667 MHz 1.050 V 0.950 V
2000 MHz 1.100 V 0.962 V
2333 MHz 1.137 V 1.025 V
So after all this I run a few tests and here are the results:
Ambient room temperature: ~24 celsius
Prime 95: cpu: 74 celsius
gpu: 61 celsius
fan: level 3, 3455 RPM
Prime 95 + Unigine Valley (gpu benchmark progam): cpu: 74 celsius
gpu: 70 celsius
fan: level 3, 3498 RPM
While browsing the internet it stays under the 65 celsius treshold, so there is no fan noise, and because I use an SSD there are no other noises either, the whole system is completely silent. It's absolutely amazing.
When watching youtube 720p videos, the temperature goes above 65, so the fan kicks in (on level 1), then temperatures saty around 65-66 celsius. Also it's interesting to note, when a video is running but I scroll down for the comments, the temps immediately start to drop, and then the fan stops, and temps stay around 63 celsius, again a silent system. It makes sense, I just never realized that videos running in the background consume so much less resources. Also when the video finished, temps drop down below 65 celsius within 10 seconds.
All in all I am extremely happy. Before these mods the fan was running constantly and loudly, temps were always above 70 and even 80 during normal tasks like browsing the net and watching videos, I didn't even try to do bechmarks, as I was afraid of frying something or doing a thermal shutdown. My temperatures are far from the ones the original poster here managed to achieve, but I didn't want to make those compromises that he did (putting the Ati gpu in power saving mode, constantly running the fan). My system works to it's full potential, it's extremely cool in laptop standards (74 celsius max benchmarking, before that was the temp for watching a 720p video and the fan was running very loud with a lot higher rpm), and the most important thing for me, it's quiet, and during light tasks it's completely silent as the fan stays off. It really is a completely different machine. If you have the patience and time, then I definitely recommend these mods, these lovely machines deserve it.