Beyond the new version number, that post is pretty short on info.  

Not quite sure what you mean. The 68060.library you better take from your Turbo board vendor. Or, failing that, directly from me. (-;

The situation is complicated... Some of the 3.9 sources have been lost because H&P never checked them back into the repository. Some of the 3.9 rights were lost because authors can no longer be reached.

What I'm trying is to find the latest possible version of all tools I can get hold of, provided that we can use it. Which is sometimes less than 3.9 (so the HDToolBox is based on the 3.1 version, just in a working condition), and sometimes more than 3.9 (like asl, diskfont, layers and the shell).

However, before this complete package will be released, there will be a "Museum version" which will be a very very minor update. Probably just the FFS and the HDToolBox.

b) Make DST work

Yeah, to me, it feels like 3.5/3.9 was a dead-end fork, and development has resumed based on 3.1. AmigaOS 4.1 is based on the 3.1 codebase as well, and AROS/MorphOS are made to be API-compatible with 3.1.

In terms of features and eye-candy out of the box, 3.9 is probably still the best, but what matters in the end is that all the tools, commands, libraries, patches etc.