OK.
A couple of things that I think will be of help.
1. Timing. I think you're concentrating too much on trying to play the chords, notes, etc. but some of it is either ahead of or behind the beat. I recommend that everyone use a metronome or drum machine for almost all practicing. Drum machines are more fun, of course.
At any rate, for an excercise in timing, set your chosen beat machine to a slow tempo around 50 to 70 bpm. First play one note/chord per beat until you're right on it consistently, then two notes/chords per beat, then three per beat, four per beat, and then back down to one again. This one's a good start which has helped me quite a bit.
For this particular tune, you could isolate one section and work to hit on time until you can do it in your sleep.
2. Notes. Yep, some of the notes don't flow so well. This is an aspect that I've been working on with bass quite a bit for the last year or so. I'm paying much closer attention to how I play each note with careful phrasing rather than trying to play out some sequence of notes for a bassline. How you approach each note make a huge difference!
Pick a note, play it short, play it long, play it soft, play it loud, play it in time, play it out of time, bend it up and down and get to know it. Get used to how you make each note sound as you play a three note passage and work up from there. I tend to think that most players dwell on scales, modes, etc. when some time spent forcusing on the phrasing and dynamics of each individual note would be better spent.
Listen to some of the great players and what they can do with just a few notes. What's more interesting to the listener, the scales or the way that the notes are played?
These are pretty simple things to work on, but seem to pay off.