So I tinkered with Audacity last night, and used the filters/effects you suggested Sid. It's still tough for me to identify and break down the fills and transitions. Maybe it's because they're not really dominant notes like the rest of the bass line. Seems that the player is muting a lot of the notes or playing the notes without actually plucking the strings (if that makes sense).
Regardless, I'm still having a hard time with it.
But I was able to identify some notes and portions with Audacity that I wasn't able to before. So there's progress!
Yes, I have experienced this as well. Try tinkering with your filter settings - cut off frequency and attenuation rate; that sometimes helps.
If you set your cut off freq too low, you lose the higher pitch harmonics associated with a note, and these harmonics are pretty important for identifying the note/pitch being played. (In the absence of the fundamental, your brain can still identify it if given the associated harmonics - mentally filling in the missing pitch.) I used cut off frequencies from 350 hz to 800 hz.
And in general, tabbing (for me anyway) is work; it takes a good deal of time and effort to get the right notes. And not infrequently, it takes me coming back to the song a couple of days after I think I've it correct, and playing through it, to realize that I've got some notes wrong still! Best of luck!
Edit: I've just redone the last half of a tab I submitted a few days ago as I didn't realize the first time through that there was a key change!
