Good one man!  I'll definitely do an article on this (or learning and transcribing in general terms...).  i can tell you for now that I've always learned that stuff by ear.  The few exceptions are the actual heads to a few Chick Corea tunes...learned those out of a book.  learning tunes to play is a different thing, tho.  Transcribing is always the most rewarding when you do it by ear!  I'll often use software to slow things down a bit if I need to, or rewind something a million times, but it's always been by ear.  The interesting thing is, I never learned any of Jaco's vocabulary or transcribed any of his solos, so I'm thrilled to hear that I did something reminiscent of Havona!!  I think the only thing I ever transcribed of Jaco's was the bass parts to "Teen Town" on the 8:30 album.  Learned that note for note when I was a kid by listening to it a thouasand times and figuring it out.  It's easiest to learn a line if you know it so well that you can sing it!
Mostly, I think we approach some of the arpeggios, etc.. in a similar way possibly?
Thanks for the question!  They have yet to post a few that I've done beyond what's on the site, so this one may not be up for a few weeks, but I'm going to write on it this week for sure.  Thanks!