I agree with others on this thread that the setup instructions from Music Man really suck. I've literally never seen this method for measuring before and, in my opinion, these can lead you to worsen your setup, instead of improving it.
I use the setup method below, which started with the fender/prs methods, plus some tweaks based on experience. This works no matter the bass, or the maker, in my experience.
First, check the bass over to ensure it's "in the ballpark". Play all the strings/notes and pay attention to any issues - buzzing, or dead spots on any particular strings/positions. If there are serious issues, you may need to address these before moving further (serious issues at this stage would be that notes don't play at all, or strings are so high that it's difficult to fret, or the pitch bends upward when fretting notes - check by playing a harmonic, then fretting the note and noting the tuning of each - they should be pretty close).
As a last step of the "eyeball check". I fret the first fret, use my thumb of my picking hand to fret somewhere between 12th and 14th fret, and then use my pointer finger of my picking hand to tap on the string as close to in the middle of the first fret and where my thumb of my picking hand is positioned. Depending on the scale of the bass and the size/stretch of your hands, this is why my thumb will be somewhere in the 12-14 fret ballpark. This does't have to be exact, I'm just trying to verify that the current setup isn't so far off that it will mess with any steps below. Typically, you want about a business card space between the bottom of the string and the top of the frets under where you're tapping with your pointer finger. I tend to think of this like - regular piece of paper isn't enough space, but thickness of a penny is too much.
Second, and can be easily overlooked = check the nut and string tree. First, ensure that strings are breaking at a sharp angle over the nut (not slightly arching/bending as they approach the nut), especially low E and B strings - if there is an arch in the string, it's likely that the string tree is too low, or the string is breaking at too great an angle over the nut, which can happen if you wind the B-string too many times around the tuning peg. This can cause tuning issues, wear your nut slots out quicker, and/or make you think you need to deepen the nut slots, when you actually don't. If this is the case, raise the string tree by loosening the screws, or remove some wraps from the string by shortening it and restringing. After checking that this isn't the case, or correcting it if it is, check the nut slot height by comparing the height between open and first fret vs. 1st fret and second fret (look at the distance between the top of the first fret and the bottom of the string, then fret the first fret and check the distance between the bottom of the string and the top of the second fret. These distances should be pretty close, or the distance over the first fret slightly higher than compared to distance over the second fret, while fretting the first. If you have feeler gauges, these can be very helpful here. Remember, if you decide to file your nut slots, you should check after each stroke, or 2, with the file to ensure you don't go too deep. If you go too deep, there's really no way to reverse this without installing a new nut. If it's pretty close, you're probably best served by leaving this alone.
Now that I've given the bass a quick eyeball check. I move into full measurement and adjustment. I think the main thing here is to measure everything the same way every time and to take note of which measurements work, or don't. You can start with factory specs (the ones below), if you can find them, but this should really only serve as a starting point and then you dial in by feel/ear.
I start by checking neck relief. Capo the first fret of the bass and fret the bass where the neck meets the body, or where the neck carve stops (where the neck starts to become square so it can sit flush in the neck pocket) - this is usually around the 15-17th frets. Essentially, you're just trying to isolate the area of the neck that the truss rod can affect and use the string as a straight edge against the neck to see how much the neck is bowing. Truss rods won't change the relief of the neck above these frets because the body/stiffness of the neck won't allow this, or these will be much more subtle than more toward the middle of the neck. I then use a feeler gauge to measure the gap between the bottom of the string and the top of the frets. This should be done as close to halfway between the 2 anchor points of the string as possible, so will likely be somewhere in the 7-8 fret range depending on which frets you're using as your endpoints, the scale of your bass, etc…. Typically, this needs to be AT LEAST 0.010'' (ten one-thousandths of an inch, or .25mm), but most commonly I am in the 0.012'' - 0.014'' range. I tend to measure this with the E/A strings. To add relief = loosen the truss rod, to lessen relief = tighten. Best to work in small increments - 1/8 to 1/4 of a turn, retune, and then re-check the measurement.
Once neck relief is set, I will set string height with the bridge saddles by measuring between the bottom of each string and the top of the fret closest to where the neck meets the body, same fret as used earlier. I favor this over the 12th fret to isolate these measurements from neck relief. I usually go with about 5/64ths on the treble side and 7/64ths on the bass side, with the other strings between these measurements so that there is a gradual slope from lowest string to the highest (on a 5 string = B string at 7/64, the G string at 5/64's, A string at 6/64's, for example). This is usually a good starting point and then adjust from there, if needed.
Once relief and string height are set, I move onto pickup height. I favor doing this before intonation, because if your pickup height is way off, it can affect tuning/intonation. With the last/highest note fretted, measure the distance between the bottom of the strings and the top of each pickup (I use the point where the pickup is closest to the string - either the pole piece, or the cover). I typically start with 6/64ths on the treble side and 7/64ths on the bass side. With the last/highest fret depressed, there is no need to set the neck pickup lower than the bridge at this stage - this will happen automatically due to the angle of the string. I set the pickups height according to the distance from the strings without any consideration to the body - most of the time my pickups are slightly heigher on the treble side than the bass side, when you compare to the body of the bass.
Once everything is at this point, I'll set the intonation by adjusting the fore-aft of the bridge saddles. Tune the open string, then fret the 12th fret. Both should be in tune if everything is good. If the open sting is in tune, but the 12th fret note is off, you'll need to adjust the fore/aft (move the saddle closer to the neck to correct flat notes, move the saddle further from the neck to correct sharp notes - I tend to use the "chase the needle" method to keep this straight because it's easy to get mixed up). Once I have the open/12 combo both in tune, I check this with the 5ths = 7th and 19th frets on each strings. Sometimes I may find that I need to put this somewhere in the middle to keep all the notes across the full neck to be in tune. Most of the time fixing the 5ths will make the open/12 intonation more accurate.
Once all the major adjustments are made, I'll play and correct any issues.
If there is excessive buzzing on one string, or if one string sounds more dead than the others (or feels flat/floppy), adjust that sting's height with the bridge to fix (higher to correct buzz, lower to fix relative dullness).
If there is excessive buzzing on all strings frets 1-5, you need more neck relief = loosen the truss rod. If there is excessive buzzing above fret 5-7, but ok 1-5, then likely you need less relief and will need to increase the bridge height to compensate.
If tuning is difficult, or the tuner jumps all over while tuning, this could be a major Sign that your pickups are too high (especially the neck pickup) and therefore the magnetic field is affecting the natural vibration of the sting. You may hear some weird chorus, or warbling sound, as notes start to decay as well. If this is really bad, you may notice a seriously negative impact on sustain, especially on the lower strings. First, if you have an active bass, ensure your batteries have good charge, because this could also cause this issue. To me, the neck pickup is the bigger culprit in this, so I usually set this one first (I tune using this pickup as well) and then adjust the bridge pickup to match the output, if needed. You can do this by ear, or by using something that has an input meter (audio interface/compressor/etc..). If you use an input meter, it's likely you may fine tune this later because you may find that although the meter reads these even, they have different perceivable output when running through your rig.
Lastly, once you have this dialed and playing how you like, take your measurements and WRITE THEM DOWN somewhere. This way, you can easily check your bass later to see if any adjustments are needed. For me, the longest/hardest setup is the first one when I get a new bass. After this, I typically check my neck relief before changing strings - as long as it's close, I don't touch it. If it's off, I adjust before changing strings. The beauty of this is that pickups/bridges shouldn't really move at all, so once you set these with the correct neck relief, they can pretty much stay as-is and you can just check/maintain the correct neck relief you have noted. If I play a lot, I typically only check these measurements 1-2 times a year just to rule out any shifts do to vibration, or screws slowly turning in/out over time.
Sorry for the length of this post. It's taken about 20 years of tinkering for me to get this system down, but it works without fail, no matter the bass.