I know that this is an old thread, but it seemed like the best place to put this rather than creating a new thread, but I just performed my first bass setup. That is to say I setup my bass myself!
Well done me 
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I adjusted the intonation for the first time today. I was about 20 cent high on the fifth fret of the E string.
One thing I didn’t expect is that the other strings went slightly out of tune once I had adjusted the E string. I figure I changed the tension on the neck. I got the rest of the strings back in tune, and the intonation is still good on all the strings, but was a bit tricky on the D string. I’m wondering if I should check the neck straightness and adjust the truss rod if needed. Is this normal?
I would check intonation at the 12th fret:
Setting Bass Intonation | StudyBass
Your bass will most probably be slightly off on other frets, unless you have true temperament frets, but those look pretty weird 
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When setting up a bass-
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Truss rod
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String height
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Pickup height
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Intonation
Tune /retune after each adjustment. If any adjustments are quite large, check all strings.
Do it out of order and you can start chasing your tail, as adjustments so wffect others as you are adjusting a system one bit at a time, thus the correct order
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