Has any one changed the value of the prewired cap that comes with EMG ciruitry to another value? From the EMG site, all their caps are 0.1 micro farad in value.
I would like to tinker and change the caps to hear what happens but I don't know where I should start and what value caps I should start looking at...

0.1uF capacitors give you a hell of a dark tone IMO.
I would stick to a 0.047uF capacitor. Some people use 0.022uF capacitors as well.

The bigger the value, the darker the sound.

What direction are you looking to go in? Since we don't know where the .1 uF places the resonance as we don't know the inductance, it's hard to constructively give suggestions. You can easily find .22 or .047 uF, etc, and fine tune it with smaller capacitors in parallel if you get slightly brighter than what you want.

I don't know what I want from the tone control yet as I do not have the pickups installed. I'll buy a few of different value and may post the results here.

the emg website used to suggest using two .1 caps in series(equals .05 or .047) as an alternative to the standard .1. thats what i use becuase it rolls off the harsh highs and string noise without killing all the highs and muddying up my tone

I have just installed the JV set. All highs do not roll off. I still hear just a very slight amount of treble there but when slapping it sounds dull (fine for me). When the tone is rolled all the way up, there is just enough to bring out the snap. The sound/tone to my ears is still somewhat vintage sounding. I replaced the Seymour Duncan SJB-1 pickups with the EMG-JV. No hum, no flab/muddiness. It sounds a lot tighter. The neck pickup has that old school sound, the bridge pickup is fat, but not too growly. Some decent EQing at my preamp (Fender TBP-1) may bring this out when I fiddle more with the semiparametric controls. I love that I can roll back either pickup and not hear any hum! Sounds rather even with no considerable dip. If anything, I may have to roll up the bass control on my preamp to achieve "my" sound. Not gigged with it of course yet, but will add to this thread when I have. In two words: "clear", "tight".