I have bought from Philadelphia Luthiers supply fret protectors and crowning file - I usually only use the fret protectors when sanding 320, if I'm feeling fiesty I might go >400 or >800, after level and crowning.
I bought A2 humbucker magnets here too. I cant believe how good the stock Agile AL-2000 pick ups now sound with the A2 magnets over the stock ceramics.
They offer custom poker chips too! Under "toggle switch rings"
http://www.philadelphialuthiertools.com/
UAAC - Best price I found for fret rocker and notched straight edge (ones side 24.75 and other 25.5" scales)
http://uaac.us/luthier-tools
leveling Beam - Home Depot 3" marble floor threshold cut into around a 15" and an 8" piece.
Found rolls of 2 1/2" wide 180 sand paper at Harbor Freight as well, 3M or Loctite spray on glue to leveling beam
fret end dress file - made from old ignition points file by grinding one edge safe
mill file, sharpening stones for fret end tangs.
Hand Reamer - $3.75 I think at Harbor Freight for enlarging or smoothing existing holes for tuners, pots, etc.
Usual hand tool suspects of screw drivers, allen keys, wood blocks, cutters and pliers, small files, hammers and mallets, painters tape, soldering station, utility knives, clamps, etc. Router as needed.
I always try to buy a Dremel, but end up using what I have pretty much just fine which kind of defeats the "I need this tool argument". I almost bought a 3000 series kit around the Black Friday sales but didnt find a good enough deal to pounce on.
Older pic with blue tape and home made notched straight edge before I cut the leveling beam down, and recent pics of Tele neck transplant:
