Prior to doing anything, make sure your witness points are set on each string. Those are the points where the string comes off of the bridge saddle and off of the nut.
You need a good break angle at those points so that the string is seated properly before you can move forward with any other concerns regarding intonation.
Also assuming that you haven't changed string gauge and that the nut slots are cut correctly.
After installing new strings and tuning them up to pitch, I like to pull on them a bit, in the direction directly away from the fretboard, to help stretch them
so they settle down. Not too much, like a slingshot
Just enough to help them settle in.
Then I re-tune to pitch and then just in front of the nut, exactly where the string comes off of the nut, and just in front of the bridge, where the string comes
off of the saddle, I press down on the string, to help create a good, crisp witness point. This way, you know that the string is contacting the nut and bridge saddle
properly and coming straight off of them in a straight, uniform line.
If I were you, I would set the B string saddle back to its original position (assuming that the intonation was fine prior to changing the strings) and start from there.
If you do a search on "witness point" you should find some good info. It's been talked about a lot.
Hope that helps.
