I just discovered this thread so I might be of some help.
I own both an original copy of Jim Hall's Jazz Guitar CD and the long out of print original Pacific Jazz LP (prior to Bock's dumb editing and overdubbing of Larry Bunker's drums). The LP is not in terrific shape, but at least plays without skips.
I interviewed Jim Hall around 1990 and he told me that the longer version of "Things Ain't What They Used to Be" was actually the master take and the one shown as the master on the CD reissue was actually Bock's edited version of the same take.
I imagine that the budget and time constraints prevented Michael Cuscuna from continuing a search for a near mint copy of the original LP (wouldn't a jazz library like Rutgers have one?), though I bet someone out there will be glad to loan a mint copy in case it is reissued again.
BTW, Lord's discography relies on the CD and has the alternate/master situation backwards, just like the CD.