I recently made the following mods to my (original series) Jagmaster:
I also found that the string height at the nut was too high: playing barre chords on the 1st or 2nd fret was very tiresome. Following the recommendations of Basic Guitar Set-Up 101, I used an Xacto saw blade to carefully deepen the slots in the nut, and a needle file to finish the slots for the larger strings.
SINGLE-COIL SWITCH. The original Jazzmaster and Jaguar designs used single-coil pickups for a clear, Strat-like tone. You can get this effect by using half of each (stock) humbucking pickup, an easy modification. I replaced the volume pot by one with a built-in switch activated by pulling the knob out. This way I can switch to single-coil mode and simultaneously adjust the volume to compensate -- all without modifying the appearance of my guitar. Here is a drawing of the new circuit. Note that in single-coil mode the "bottom" half (Neck B) of the neck humbucker is active and the "top" half (Bridge A) of the bridge humbucker is used. Thus when you set the 3-way selector to use both pickups in single-coil mode, they have a humbucking effect together (like Strats made since the 1980's) to reduce hum and interference.
PICKUP COVERS. I like the look of chrome pickup covers, though supposedly these can have a slight effect on pickup brightness. I ordered some Schaller ones which fit the pickup rings perfectly (just add a bit of tape to keep them from rattling or sliding off), but the cutouts in the pickguard didn't quite accomodate them.
CUSTOM PICKGUARD. Rather than messing with the original pickguard I decided to cut my own pickguard. I don't like the shape of the stock pickguard anyway -- it looks like they started with the Jazzmaster pickguard and hacked it around the modern tremolo bridge assembly of the Jagmaster. It looks lame, IMO. I don't have access to power tools, but shaped my new design with heavy scissors, coping saw, and sandpaper. After painting it I found that it looked much nicer with dark-colored screws purchased from a hardware store. The photo above is my new design, which *even* my wife thought looked much better.
It is painted a very dark purple, with rainbow-effect metal flake applied over this in clear acrylic. Email me if you want some of this metal flake powder.
In case you want to make one, here is a template of the pickguard, and here is the other half. Print them out separately and match them up according to the screw holes. They were scanned at 75 dpi, so you may have to adjust the magnification when printing.
Schaller humbucker covers, 500k push-pull volume pot, .06" blank pickguard material. These were purchased from Stewart-Macdonald, about $30 total.
You'll also need shielded, small-diameter two-conductor cable, heat-shrink tubing, and soldering equipment -- available at Radio Shack.
Check out Jagmaster Zone.