I finally updated to SVN Revision 354 yesterday. I hadn't noticed that there were new revisions, so apologies for posting so many issues from Revision 350.
After some "Play Now" games to clear things, I selected the modules I wanted active. I had several crashes on startup, but was eventually able to start a game. Later after exiting it took several tries to reload a saved game. Today, though, I was able to reload a saved game on first try. What I've started doing is saving the game before exiting, instead of trying to reload the most recent Autosave.
Just a few issues:
1) I got a python exception -- again -- from the "Form Empire" event (I think that's what it's called) and the game went into a hang, so I had to force-close. I think this is the Minister Koun event, right? It doesn't always cause problems, I know: I reloaded an earlier saved game and was able to play through, eventually encountering Minister Koun himself.
2) The Mekaran leader Zaria Scheras is listed as an Emergent Leader but her Trait, Caretaker, doesn't level up. It might be easiest to just switch her to being an Important Leader so she can acquire a second Trait during gameplay. I'm not sure what actions would level up the Caretaker Trait anyway, maybe building the corresponding units? Or what Levels 2 and 3 of the Trait would provide.
3) I'm playing as Mordmorgan of the Lanun. Level 2 of the Virtuous Pirate Trait says that naval units get the Trade Defender promotion, but there's no description of that in the Civilopedia.
4) I disabled the Frozen module but the No Liberation option was still available under Custom Game. (In the past I would have the Frozen module active and select No Liberation, but I figured disabling the module was easier.) I don't know if this causes any issues or conflicts under the hood, but if so, it might make sense to link the No Liberation option with the Frozen module, so the option is available only when the module is active.