Just giving an update here:
Pickups - All of the electronics were gone over by a tech and there were no issues (pots were as stated: CTS 1meg, and cap was .033uf orange drop). We put in a .01uf cap to see if it made a difference. I ended up purchasing a Seymour Duncan Antiquity II for the neck and soldered it in last night (the first time I soldered anything other than a pair of speakers!!!).
IT SOUNDS AWESOME. Has the exact tone I was going for in my head (warm yet jangley, very balanced and tight but still with plenty of harmonic overtones, full but not overwhelming in the bass/low-mids, upper-mids have a tiny bit more bark). I really ended up liking the sound of my pickup wizard neck pup with the formvar wire and I think it's a great pickup and I highly recommend it for those seeking to replicate the late 50's-early 60's JM tone. I actually compared it to a bunch of early 60's Jazzmasters in nyc guitar shops and the Pickup Wizard neck pup (and my guitar) actually sounded better than all of them (no joke). I just had more tone and more resonance (though the mastery/setup prob have a lot to do with that), but I think the thicker "C" shaped neck on mine really gives it a lot of warmth and fullness.
The Antiquity II in comparison to the Pickup Wizard with Alnico 5 and Formvar wire did exactly what I wanted it to do...reduced the bass/low-mids, tightened up the bass/low mids, and added a little more presence to the upper-mids/treble. Overall, this really enables me to have more clarity and tightness (aka not as muddy) when I play power chords, stacked 4th's, and non-perfect intervals (i.e. maj7, b9, b5) on the lower E-A-D strings, ESPECIALLY when I use my Hoof Fuzz. VERY HAPPY!!!
I'm gonna prob see how the .033uf sounds again and reinstall it sometime this weel as well.
Set-up: I showed it to some JM enthusiasts/techs at some nyc shops and they all said it looked pretty good, but I should reduce the shim a little, lower the bridge (obviously if I lower the shim), give the neck a little more relief, and have the frets leveled/dressed. So, I took out some of the shim (it was up to 1.84mm, now down to 1.14mm), lowered the bridge, gave the neck a little more relief (had to try it 2-3 times until I found the perfect amount), reset the radius on the bridge saddles back to 9.5". It sounds and plays very nicely, though I still am getting some buzz, and I wish the action was a little bit lower. I'm gonna end up taking it to someone eventually to have the frets leveled/dressed and I think that should be the end all of it (until I decide to put a Novak JM-90 or JM-180 in the bridge