How flat is it at the 15th fret?
Intonation is simple enough to adjust.
1) A tuner
2) A screwdriver or hex wrench (I think you need a screwdriver for the MM adjustment)
Here's how to do it:
1) Check tuning of open string (i.e. not fretted) adjust if necessary
2) Check tuning on 12th fret of same string
3) If 12th fret is sharp, adjust the saddle so that it moves back (effectively making the open string longer). If flat, adjust the saddle so that it moves forward (effectively making the open string shorter).
4) Repeat with step one until open and 12th fret are both in tune.
You'll never get every fretted note to be in perfect tune, so don't even bother.
Here's a link: http://www.tunemybass.com/bass_setup...ntonation.html
There's other info on there so you can learn how to do your own set up.
You will only need a few tools (doing a set up on a Music Man is really easy because of the truss rod wheel). And, it's not very complicated, so long as you understand what you're doing, and why you're doing it. The most "dangerous" thing is adjusting your truss rod, adjusting too much can really screw up your neck, but if you make small adjustments, it shouldn't be a problem, unless you have a serious problem with your neck to begin with.