Thanks for the great info. I'm still using the original stock strings (10s I think) but am planning switching to 12 or 13s once my replacement jtv-59 arrives next week (instrument I received was the wrong color). First thing I did was reduce the global string level using the lester models, ending up with somewhere between -10 and -12 db. For me the 1 and 3 strings were louder than others.
So far I'm impressed with the strat, tele, and acoustic sounds, less so with the jazzbox and semi sounds. I've spent several hours trying to get a decent jazz sound (I'm mostly a jazz player), tweaking everything including pickups, bodies, polarity, tone resistance/capacitance, etc. but haven't really found anything usable thus far unfortunately. The inconsistency of the 6 string, very noticeable piezo nasally quack of strings 4-6, and the inability to tweak the EQ of individual strings has beaten me down so far. I absolutely love the ability to change tunings on the fly though, that's the killer feature for me.
Anyway, I'll report back when I get my new axe and string it up with fatter flatwounds. I realize that it's not the recommended setup and likely will destroy any semblance of authenticity for the other models but if I can get a usable jazz tone that will be good enough for me.