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This has been most helpful!  Apparently, a new script I added to stop the timer whenever you're reading something or sitting through a cutscene has been messing with how the New Game+ works.  I've fixed all of the issues you were having with the timer running out during battles, as well as the hopeless loop all New Game Pluses were getting caught in.  I'm going to see if I can somehow rescue your New Game+ file.  

The bug that happens when someone leaves your party is a bit stickier, though.  I'm trying, but I can't seem to fix it.  I think it's an issue with the Yanfly script not playing nice with some other vital scripts.  I'll spend some more time on it, but it might not be fixable.  

Happy to hear that the NG+ issue seems to be fixed!

For the other one: if it can't be fixed, it might be worth trying to avoid it. If the clinic is the only situation where that bug is likely to appear, it could be worth checking whether the selected party member is in the active formation or not. If it is the case, denying that "service" would probably avoid the problem. It would reduce the player's options, but it might be less obtrusive than a crash.

I'm not sure if there are other points in the game that lead to the same problem. There is at least one scene where a party member leaves for good and a related character takes that place, but that didn't cause any problems in my playthrough. Not sure if that character was in my active party at time, though.

A more general approach could be a loop that opens up the formation screen if there are fewer active party members than there could be. In pseudocode, it would look something like that:

// After you lose one of your active party members
possible_party_members =  (4 or number of total party members, whichever value is lower);
while (active_party_members < possible_party_members)
    show_message("Please fill up the blank spots in the formation.");
// Loop is done when the player has filled up the active party

On the other hand, the players lose the ability to battle with less than four party members, once their party is big enough...if anyone wanted to do that.

And don't worry about rescuing the file. I've already played through the complete game in another run, carefully avoiding the situations that might trigger those two bugs. It took a bit of extra effort, but it was worth it! =)