It's okay to open the BFL to change fans, re-apply thermal paste, etc. If it's at 40C you should be able to run a faster firmware.
Did you move the BFL after you ran AutoTune?
No, didnt move it at all! It likes where it is
I dont know maybe an error with autotune.
I'll just leave it alone for know, make as many coins as I can before the reward halves