So I am finally done futzing with my SVT-3 Pro...
I have to say, NOW I am impressed and very happy!
I did 3 things:
1) Complete retube. I went with eurotubes.com and ordered 4 standard JJ ECC83S tubes to replace the 12AX7's, and 1 JJ ECC82 for the 12AU7. There are options within these choices, but I went with the "standard" tubes. I dealt with Jay who was very helpful and thorough with explaining all the options. The improvement is nothing short of AMAZING!

The amp literally came to life. I have more gain, but I didn't lose ability to get a nice clean tone (which was a concern). I also have much more overall volume (which I believe is due to the ECC82?). I no longer need to engage the EQ and bump the EQ level slider to get more volume. The tone is rich, warm, fat and punchy. If I want growl, I can get growl (although at the moment I still like my SansAmp Programmable Bass DI for the dirtier tones). The fan seemed to run a bit slower after the retube (albeit still noisy). It still ramped all the way up when the amp was first turned on, but it gradually slowed down to the point where I didn't hear the motor anymore, just the grinding sound I described before.
2) Replaced the fan. There was definitely something wrong with the original one. The (exact) replacement is by no means quiet, but it is a significant improvement to the degree where I'm no longer distracted by it when playing at low volume (the grinding noise is gone).
3) MOSFET bias. I read here in the forums that the 12AU7 is what feeds the MOSFETS, so I assume that replacing the 12AU7 (if not all of the tubes) had an effect on the amount of signal feeding the power amp section. I did notice some very low "solid state" sounding distortion/fuzz after the retube, which sounded exactly like what others have described on the forums. I carefully used a plastic potentiometer adjustment tool and nudged the MOSFET bias pot ever so slightly clockwise until the fuzz was gone. It literally took a hair's thickness of a turn. Since I did it by ear, I would like to try and find out the procedure for doing this with a meter (i.e., the right way) so I know it's correct for my new setup. Can anyone help in that regard?
So there you have it. Thanks to all the people here on TalkBass for your replies and helpful suggestions!