String placement over pickups

I think this is actually two separate issues:

1. Yes, it's always best for the string to pass in between the pole-pieces but not mission critical (it's also nearly impossible to get the string path to line up exactly with both pickups). You can certainly change the saddles on your bridge to threaded saddles which will allow you to move the string over in very fine increments until you find the best string path over the pickup.
   
2. The chorus on your E-string is probably because the string got twisted when you re-tightened it after changing your pickups. Loosen the string and tighten it using the tuning peg (in other words, don't do the first wrap by hand as this can cause twisting). If that doesn't fix the problem then the E-string is probably bad. The twisting effect can separate the string's core from the wrap wire causing all sorts of nasty sonic artifacts.

 

yep, and yep.

you should be able get the spacing close to right with the stock saddles, since they have multiple grooves. (i do hear a difference, especially when the pickups are closer and you dig in like i do, but it's not a deal-breaker.)

to untwist the string, loosen it til it comes off the tuner. it might immediately spin around a time or two, at which point you can slip it back onto the post and re-tighten.

 

It sounds like your neck pickup may be too close to the string. The magnetic pull can cause a pulsing sound in the upper register of the lower strings.

 

The distance from the pickup should be measured while pressing on the top fret I believe. Try lowering the pickup and see if the out of tune sound goes away.

 

Pickup height is a matter of preference and will vary based on the pickups and strings being used so don't treat the Fender numbers as gospel. They are just a good starting point. Your ears will be the final judge.

The only helpful tip to remember is that sometimes you need to lower the bass side of the pickup a little more than the treble side in order to achieve the best balance across all 4 strings.

 

To be thorough you should crank your amp up and lower the pickups in small increments (.5-1mm) and see what sounds best to you. You'd be surprised how many people like the sound of their pickups lower than Fender spec.

 

i like my own higher actually (i say my own, i don't typically set customer basses that way), but you should definitely take some time with your amp and a screwdriver, to play with the height til you get what you like.

a big part of the process is getting the output balance right, so that each string is as loud as the others, and so that the neck pickup is the same volume as the bridge. you'll have to do it rather than a tech, because your own rig and playing style matters here.

on your bass, unless you tap up the polepieces so that the middle pairs are a little higher than the outer pairs (something you can do with american standard instruments with no problem), it will mean dropping both pickups a bit, especially the neck pickup on the bass side.