Actually, I don't think I can put the thermistor on the transformer after all. There is something going on when I put it there because the circuit is behaving strangely, but only if I put the thermistor on the transformer, it's fine when I put it on the heat sink, so I think the heat sink it is. Does it even matter that the heat sink is at high voltage, I mean the thermistor is completely electrically insulated from the heat sink?
When I say the fan circuit is behaving strangely when the thermistor is connected to the transformer, sometimes the fan speeds up when I lower the current, sometimes it just turns on all the way and won't go off (this is eerily familiar to when I had the other temp control circuit going and was getting noise interference...). Now, when it is doing this, that is slowing down when I turn the current up, if I take one side of my volt meter and touch it to either the negative input of the op-amp or the ground of the op-amp it seems to negate the effects of this interference and the fan speeds back up to the normal speed it would be at if I didn't have the current turned up. Another strange thing is I have three thermistors wired up for testing purposes, two on the heat sink with different epoxies and one on the transformer, if I have one of the ones on the heat sink plugged into the circuit and then just touch ONE of the wires of the thermistor on the transformer to the negative input of the op-amp the output voltage of the op-amp go up = fan speeds up. This seems very strange to me because I am not even making a complete circuit by just touching ONE of the wires of the thermistor to the negative input. As if all that wasn't strange enough, it seems to only be doing all these things when it is colder because last night when it was running for a while I didn't notice these issues.
This is all very strange, I would be interested to know why it is doing this as some sort of science experiment if somebody knows, but it is purely educational as I am just going to attach the thermistor to the heat sink. All the above problems go away once the thermistor is not touching the transformer.