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You seem to have a knack for finding really strange bugs somehow.  Well, thanks for your report, I'll noodle around and see what I can do.  So far, I haven't managed to replicate any of the bugs you've described, but I'll keep at it.  

I could send you my save files, if you want to. For the TypeError, I simply did what I already described.  I have one save file before the party member is removed and another one after that, right before a battle that crashes the game.

I think I also found the source of the NG+ bug. The problem wasn't the counter itself, it had something to do with the protagonist dying in battle before escaping. Her dead status seems to carry over to the NG+ and leads to the game noticing that the whole starting party is dead on the first map, prompting a game over screen. It could probably be fixed by healing the whole party in the "timer's up" event right before it asks you to save for a NG+ file. I also have two save files for that, one right before a boss battle with about 30 seconds left. Just let the protagonist die (or use the Hemloxxx item on her), wait until the timer runs out and then escape. It then asks you to save (which I did on another file). If you start a NG+ from that file, it immediately leads to a game over.

Ah, that's weird!  The NG+ is supposed to recover everybody's health on its own, but I guess if it doesn't, then I can do that manually.  Thanks!  

And if you could send me your save files in a Dropbox link or something, I will gladly accept then

Alright, I uploaded the save files (including a description) here:

I'm glad I could help~

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! =)