I paid 40 bucks to get my bass setup, only to re-do it myself 2 days later. I recently bought a 6-inch steel ruler from General and it's a good thing/bad thing. I've found myself to be constantly adjusting things now that I figured out little things on my bass, like my A and D strings are half a milimeter further away from the pickup than my E and G strings.

Great, now I have to clear my schedule for the whole weekendAlso I agree with VintageBT6Lover but I use a $85 Boss TU-12 (has an analog meter on it) for intonation.
I don't use the 12th fret harmonic for intonation. I actually check all the dotmarked positions. I will compare open with 12th and see if the meter moves appreciably. Then I check the 3rd fret and the 15th, 5th and 17th etc. If the meter moves less than one or 2 cents for each note I know that i am close.
In general the smaller strings are very easy to get REALLY close to perfect intonation. The A sometimes is a pain but I can usually get it pretty good. The E (and B) strings are usually impossible to get perfect intonation so I usually only check up to the 15th fret and the rest after that usually end up getting progressively sharper. I have only seen one bass that I remember having an almost perfect E string and it even had 24 frets. My Jack read Custom short scale.
Some tips: If you are going to intonate, you might as well plan on having those strings on there awhile. As soon as you change brands or guages you will need a slight adjustment.
Do the setup in this order:
Change strings (or be comfortable with having them on for a long time after)
Truss rod relief (hold down string at first and last fret. credit card thickness visible under 7th fret)
Bridge saddles (follow the curvature of fingerboard. Thicker strings need progressively more space off the last fret)
Microtilt or shimming if needed (this can be tricky)
Nut filing (when you fret the first fret the string should optimally move no more than when you hold down at the 1st fret and fret the 2nd fret.)
Intonation (forget about harmonics and check more than one spot. I do all the dots)
Pickup height (usually slanted so that the G side is closer to the strings and the E further away. best thing you could do is set your eq flat and record yourself on a computer (direct) and look at the height of the waveforms for each string in most sound programs. Adjust accordingly.)


