Just some background - I've been playing for a little over a year, took lessons for about 5 months of that and have been in a non-gigging "fun" band for 8 months of that. Not a pro, just a hobby. I use a Fender Jazz 5 String for this.
I have been struggling for a few weeks to get this down cleanly at the correct tempo (about 85 bpm). It's the intro, verse 1, and verse 2 bassline.
http://www.youtube.com/watch?v=6G7ZLaiPxu0
Obviously I can play it slow just fine. My question is, am I playing it the most efficient way or is there something I can do technique wise (besides extensive practice, obviously) to get it cleaner?
I start with my 1st and 3rd finger on C# (fret 6 on G) and D# (fret 8 on G) respectively. I stay in that position for that particular bassline other than a tiny shift with my index finger to slide G to G# in one section. I start plucking with my middle (2nd) finger instead of my first - I usually learn the other way around but for this song I didn't for some unknown reason.
My biggest hurdle is when the bassline goes between A# (fret 8 on D) and C# (fret 6 on G) twice in quick succession. At first I used to actually pull my fretting fingers off those notes but I leave them there now and just pluck the two strings, being careful to try and avoid my fingers accidently muffling either string (happens sometimes where my D finger will muffle G a little).
I get that part down but the last C# is often very soft or non-existent since I'm hurrying to hit F or D# (fret 8 or 6 on A) and I just don't get a good pluck on G. My plucking order ends up being:
A# - 1
C# - 2
A# - 1
C# - 2 (problem child)
F/D# - 1
If that isn't a good explanation I could probably make a diagram or something tonight after work.

Any advice for improving my technique on this song?