At first I wasn't going to fix this because there was no overlap between CDs 2 and 3, but then on a faint hope I went to archive.org looking for a suitable AUD for patch material; sure enough, I very tasty purported FOB of set 2 is sitting there, ripe for the download. I say purported because it's extremely clean, and per my ears and comments both on archive and etree it's most likely a board or matrix. The only flaw is Branford is either very low or missing entirely during space, where in the Miller seed he's very prominent.
I used this source to patch in about 15 seconds of missing space between the end of CD 2 and the beginning of CD 3 (1:06-1:20 on the new d3t01) using CE Pro. Shntool was used to correct resulting SBEs and the SHNs were converted to FLAC (I was going to reconvert them back to seekable shns as they were originally, but after reading about the problems some people have with them I decided on the flac route).