I will probably be of no help...I know what you're talking about - I think many people have the same problems with Bach. My solution to these issues has been to understand the counterpoint, which makes it easier for me to choose fingerings, and to know how to interpret each piece, but you're probably looking for a quick fix, huh?
Many of the elements that you mentioned are a matter of personal interpretation - there are "correct" ways to play Bach, but many in our era think that if Bach is played on piano, it should be adapted to the instrument, rather than played in strict baroque performance practice style.
Once you sort out the awkward fingers...definitely hit the metronome. Bach needs much metronome luv.