When I tune with the tuner, the B string never seems to sound right. I usually adjust the B string by ear, then I'm happy.

It's easy to overlook the simple approach to these problems.

Like a lot of people I have a hard time telling whether a string that's off is a bit sharp or a bit flat. I find that if I play the strings and sing the notes they are producing, then I can feel the difference in my throat. The throat tightens for a string that's sharp and loosens for the string that's flat.