...
I honestly thought my mod was rather bug free as I didn't hear of any problems other than maybe the replace lost limbs problem

Ok, I'll try to address your problems as far as I can.. (Not at home right now, so can't take a look at your savegame)
Your first issue: You tried to deactivate Mai? Did you read the description? Mai, once activated, doesn't like you to mess with her programming, so will rather initiate her self destruction then let you do that.
Sorry, but that is intentional and I'm not sure I want to change that for now.
Second issue: That sounds like a bug with my code to replace the lost limbs. Normally it should replace the lost limb with a limb that has a health of 1HP. To do this I create a new limb and add damage to the limb with a count of (maxHealth - 1). If your Mai dies of it, then I missed some critical changes of the limb and health system in a12. it did work in a11, but their was a big change and it Looks like I missed something important here.. Sorry, that is really a bug of my work.
Third issue: The nanite repair station is effectively a renamed and retextured Hopper. I'm not sure if I can locate the problem that's causing the Job loop, but I'll at least try to find it.
Fourth issue: To be honest, I have no idea what would cause the savegame to get corrupted, but I'll look into your savegame and try my best to find the root of this.
The cleaning bot issue: The cleaning bots use the vanilla cleaning tasks. So if your colonists will clean something, then the bot also will clean that. If you colonists won't clean something ...
The only idea I have why your bot didn't clean something is, that it may not be inside the cleaning area (homezone)? The range of the bots is only defined by this: They'll return to their base if they are further away than 50 cells and their battery is < 50% (I'm not 100% sure about the values yet. I must look them up at home to give you an accurate number)
All in all I'm sorry that you got some gamebreaking bugs and I'll definitly look into them.
If I can't find a solution for the Mai-limb-replace-bug, I'll at least remove the nanite assembler until I find a working solution.