This should help : http://www.ernieball.com/faq_mmbass.php
Look under "Q: How do I set up my Music Man bass?"
I advise not to ajust the truss rod unless your really sure about what you're doing. If you do turn it very slowly, as the difference can be big after even a small turn.
There was a thread on this some time ago now....I can't find it at the moment, but this was my 2 cents worth:
This is how I see it (my opinion only):
First of all, there is no dial-in string height nor truss rod setting. The instrument has to be adjusted to each individual’s own playing style.
Make adjustments in the play position so gravity doesn’t enter the equation. The best way is to be seated with the instrument on your lap.
Adjust the truss rod to get the neck as straight as you can. Turn the truss wheel clockwise (as you look from the heel of the neck towards the headstock). To be on the safe side, loosen the strings between each adjustment and retune to pitch. Use a finger of your fretting hand and depress the E string at the first fret. While doing this, use the thumb of your right hand and depress the E at the 12th fret in such a way that the middle finger of that hand is pointing towards the first fret and use that finger to depress the string at the 5th or 6th fret. There should be a paper thickness gap (or even less) between the top of the fret and bottom of the string at that point. That’s the starting point for the neck.
For a comfortable feel of the strings, their height should reflect the radius of the neck. At the 17th fret, measure the height of each string between the top of the fret and the bottom of the string. Using a 6’ steel rule, aim for 3/32” on all strings consistent with no fret buzz and comfortable height. Depending on your playing style, you may be able to set them lower or may need to set them higher. Tune to pitch and check the strings all up and down the neck.
If you find the strings buzz at the first few frets only, begin adding relief to the neck by turning the truss wheel, in small amounts, counter clockwise until the buzzing goes away. There’s no need to loosen the strings for this adjustment (you’re loosening the tension). That is your truss adjustment.
I usually like my strings slightly lower than the preceding ones. After setting all strings to the same height, I lower the G ¼ turn and lower the in-between strings (A & D) down proportionately to meet the G.
If you feel excessive resistance on the truss wheel, don’t proceed any further as you could permanently damage the truss rod. Take it to a tech.
After adjusting your action you should readjust the pickup. While depressing the E string at the last fret, measure the distance from the bottom of that string to the top of the pickup magnet for that string. Adjust for a distance of 4/32 inches. Do the same with the G string but, this time, aim for a distance of 3/32 inches. Final adjustment may have to be made to the G side by ear, so that the volume is even across all strings.
That's the way I see it Peter...especially in relation to setting the relief. There's so much conflicting info. Heee heeee...all those hours of sitting there with a capo on the first fret and a feeler guage trying to set relief at .015" because an article said that was the magic relief...kids looking on....wifey looking in occasionally...thinking I've lost the plot...LOL
PUP height...they're Fender specs. Although EB describe a different way of setting PUP height, it works out the same. They appear to be only nominal measurements anyway...to get a person in the ball park. I know guys who set them flush with the pick guard and others who set them higher.
String height is obviously a matter of how heavy or light you play. One luthier I used to go to (I don't any more) always insisted string height had to be 4/32"...no ifs...no butts.