Sam,
Going back to a prior version the run time was about 1 minute. That version used JoinAcross 12 time. My current version takes about 10 minutes and uses JoinAcross 15 times, plus there are some other changes. The Stack Exchange post that I had referenced has some other benchmarks. The lists of Associations that I'm joining have lengths of about 9,000. During the run I can see that the steps with JoinAcross is where the additional time occurs. Also I did run some tests, some time ago, with just a JoinAcross, but I don't still have those results.
I'm running Windows 7, 64 bit, Mathematica version 10.4.1.0.
