Here's what I do for setting pickups' height. The most important thing to notice is that the thinner the string and the nearer to the bridge, the weaker the response and vice versa:
1- Set a proper neck relief.
2- With a 6" steel ruler, I make sure that the measurement from the top of the 12th fret to the bottom of the strings is 3/32".
3- Then I set pickups height as follows: Neck pickup: 5/32" for both bass and treble sides. Bridge pickup: 1/8" (4/32") for both sides.
4- Lower the G string by 1/64" and raise the B string by the same amount.
Coincidentally, I've just bought a bottle of
Loctite 242 threadlocker (medium strength) because the screws of my Bongo's pickups keep loosening and the pups are always raising. It turned to be a very annoying thing and that's the best solution for it (according to EBMM customer service).