As of trunk@7803, I’ve fixed the last major problem I know of with post-3.1 code I’ve written. You should be able to use the svn7803 builds successfully. If not, PLEASE report the bugs you find.
vassalengine.org/~uckelman/builds
Now that I’m (possibly) finished with the new code I was writing for 3.2, I’ll start rounding up things which need merging.