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Based on that then I have a few pieces of advice. I will start with saying that I do not think anything you find strong from UC and UM are that bad but I doubt my opinion matters to you on that. They have been out for so long now that it is core part of the game as with all the other core line books. People play PF for choices and more books give that. Anyways on to the advice.
Even if you did not allow MP, they would have found a way to get BS to get to the same point. It's just the nature of the spells. You should ban polymorph from the game. That would solve your problem right away. There would be no more OP characters since all their damage would drop off big time but then you are going to have to go back on a lot of the changes you have made to the monsters. This also comes with the price that the players may not be happy. If three people are doing this together then they seem to like it.
You could remove the three players that are giving you a problem. The general advice is that you remove problem players from the game but then you have to look for three new players which I doubt would be very hard since there are always new players but that comes with the unknown of what those players are like.
Then there is the third choice. If these people are your friends and you like playing with them. Change systems. Do it now. The longer you wait, the more headaches you are going to get since it seems like PF might not be what you are looking for from a game. On this front, I can offer you other games to play but I am not really sure what you want from a system so I would need that info from you before I offer anything on that front.
The key to all of this is to have fun right? From what I see here, you are not having any fun and I can't speak for your players. I would be careful in thinking you know what they want though. Depending on how well you know them, they might not be saying everything on their mind. People do not like to confront others. It's by nature and you can see it all over the internet when players and GM talk about problems in their game that could be solved with talking.
I want to help you make your game a better game but I think house-ruling is the wrong way to go about it. It causes all kinds of problems the more you add. That includes messing with the monsters.