John.
In my opinion you should start with the basics. First read carefuly the PHD2 documentation. Then…
For first: change the guiding algorithms and parameters. For EQ6 (I use one with N150 f/4) the best results are achieved with the predictive Pec algorithm for the R.A. and the Restistance Switch for the Dec. Also, never guide with 100% aggression. Mounts need a bit of relaxation (around 20-30%) especially in R.A. axis. So the 70% agressivity is good enough. For PredPEC use default values. This will avoid the bouncing effect clearly visible in the PHD plots (especially in R.A.. The guidnig star is bouncing up and down step after step. Also, determine the minimum star movement parameter at which correction is necessairly. The guiding assistant will help you here.
Next, align the mount fairly precisely with the celestial pole. However, don't overdo it – never directly to the pole. An accuracy of 1-2 minutes should be fine. The tracking accuracy will be very good but this trick will help you to avoid backlash problem in the Dec axis – the mount will be drifting only in one direction. It is very easy to correct with RS algorithm. Perform a good calibration with plenty of steps around the local meridian and the celestial equator.
If you do not dissasemble guiding scope from the main optics you do not need to repeate the callibration. It will be good enough for next time assuming the mount will be placed to the celestial pole with a similiar precision and guiding scope angle is the same.
At the end check the cables route. It may affect the tracking accuracy.
These are the basic things you need to do.
About the 2600 vibrations. I wouldn't worry about camera fan vibration affecting guiding accuracy. If you're observing this effect in the main scope, you won't see it in the guide scope (probably f=120mm) with a 2-second exposures. Firstly, the scale is completely different (instead of 1"/pix, you have 3-4"/pix), and secondly, the vibration frequency is very high and shouldn't affect star centroid from one guider image to another.
Hope it will help.