I am in the same boat as you, I have a stock JD-100,and I want to mod it as well. I have never heard a modded unit, but I can't imagine why a moderate mod would make it sound worse. I rolled my stock Sovtek tubes, for some RCA 5751's and/later Sylvania 12ax7's, a minor improvement. The JD 100 has 4 el cheapo WIMA output/coupling capacitors after the tube stage, which are the only other important mod really IMHO. I really would like to put in some Hovlands, or some other highend cap. Years ago, I has Parts Connexion do an upgrade for my Anthem Pre 1 tube Preamp) which changed these SAME Wima caps for some Infinicaps, an incredible improvement. I suppose some better resistors, diodes might improve the power supply, but I want the most bang for my buck-- the wire, jacks, etc. seem very good quality to me, and the clock "upgrades" I am really wary of. I will probably use Response Audio for my mods, as he agrees with my theory and puts most of the money in the VH Teflon V-Caps.
Rest assured that the JD 100 is a great bargain and a wonderful, musical product. There is nothing else I know of near the price with a genuine tube output stage, instead of a bogus tube buffer. NO OP AMPS is a huge "mod" designed into the player, would you put op-amps in your Quicksilver Preamp's output section? The stock unit (with NOS tubes)has a wall to wall soundstage, harmonic richness, and makes music sound alive. Change out the caps and you (and I) should have a unit that will really be superior.