I play that section (two choruses) as A6/9-D9-A6/9-E9-A6/9 with the roots at the 12th fret (A6/9), 10th fret (D9), 12th fret (E9). I then play it higher as A6/9 (17th fret root)-D9 (17th fret root)-A6/9 (17th fret root)-slide down to E13 (or E9) (12th fret root) and keep sliding to A6/9 (5th fret root) and/or A (root position). It's basically only 4-5 different shapes, as you're playing the ninths either with the root on the 5th-string or 6-string, the 6/9's with the root on the 5th or 6th strings, and the 13th with the root on the 6th string although for all these chord he's probably mainly only playing the top four strings. These chords/chord moves are a big part of his repertoire, especially at the 2004 R.I.B. show (Double Talkin Baby, 20 Flight Rock, etc.)
Hope that helps ye out.
Capt. Jones