To me it just sounds like both of your fans have problems.
There were two Lenovo fan FRUs for T60 with discrete graphics:
41V9932 - Originally released for Core Duo models
41W6407 - Originally released for Core 2 Duo models
Both fans are completely interchangeable and I've seen the first used on C2D models, as well as vice versa.
The differences between them are emphasized in this picture:
http://img823.imageshack.us/img823/4723 ... 1w6407.png
It is suggested (and informal experiments someone support this theory), that 41W6407 is better for CPU cooling, while 41V9932 is better for GPU cooling - the reason is in the heatpipes. The CPU heatpipe on the 41W6407 reaches both vents, so gets cooled better, however it comes at the expense of the GPU heatpipe which no longer enjoys direct exposure to the vent as it does in the 41V9932.
However, both fans when operating well should be more than adequate for a T60 with X1400. I used to have the 41V9932 on my T60 w/ X1400, which died and was replaced with a 41W6407. It seems to me that the CPU temps are a bit lower now, and the GPU temps are a bit higher, but the difference is maybe ~3C each way. I have never had any problems with the machine locking up due to heat, with either fan.
With that said, I have the 15" T60, so the larger chassis may be somewhat better ventilated. Quite a few people suggested various modifications to the heatsink (from applying better thermal grease, to using custom-made copper shims for the CPU/GPU cooling pads). You can find a lot of talk about it in the forums.
