I owned a TRB6 and it sounded very similar to my RBX6JM's stock sound (I am guessing that since John Myung played TRB's he used that sound as a model). I have replaced the preamp in my RBX with both an Agular OBP-3 and an Audere 4. The OBP had a lot of lows and smooth highs with a better fidelity than the stock preamp, but it did not quite have the midrange I wanted. The Audere is like playing through a window. It is 100% transparent, absolutely no coloration. Basically, any sound you make acoustically is exactly what you hear amplified. It is even more clear than the polyfusion in my Zon. Plus, with the 4 band and Z modes you can dial in just about any tone you want. If you are wanting a modern hifi tone the Audere is the preamp to get. If you want more of an old school round tone lean towards the Aguilar.
As for replacing pickups, Yamaha uses odd ball sizes, so it may be a difficult search finding a correct fit. Your best bet would be to get some custom made by Aero.