I have one of these. Play it first; you may rethink upgrading. The pickups and preamp really sound good. (I did have an issue with the MM pickup and opted for a Nordstrand MM5.3, but this change was not about tone.). Tone-wise, different pickups will make it different, but "better" is subjective. I always wonder why peope plan to change electronics in a bass they have never heard, but I suppose you have your reasons.
As for the machine heads, I do not know if Hipshot makes a direct replacement. The ones on mine are of such quality that replacing them would be pointless.
On my bass, I installed the Nordie MM5.3 and a set of Loxx strap pins. I have no plans to change the J pickup (it sounds great!) or make any other modifications.
Be sure to post pics!