Butterscotch...you sound just like me. I thought I was the only one who constantly worried about my babies and always wondering "what if". Glad to know I am not the only one! As for your male putting his head down, he was "presenting himself" to you. When a rabbit lungs forward and puts their head down they are asking for pets. So, you he was not angry with you for petting him, it's exactly what he wanted. The more you pet them the more they will do this. When I walk into my rabbit's area they all run over and put their heads down as they know they are going to get some love from Mom.
Your little girl sounds a lot like my youngest girl. She is a little stinker. I came home one day to find her on top of her cage, how she got their I have no idea. I have two pens kind of side by side with a walkway down the middle. They have the entire room, one side for one pair and the other for another pair. Two bonded sets. Lily, my little stinker is constantly trying to escape to go see the other rabbits. She is convinced they have better treats on their side of the room. I have had to put up all kinds of odd barriers to keep her in her own area. I just make sure she has lots of toys and space to run to keep her occupied and avoid escaping. It's been a while since she's gotten out, so I think I finally got it taken care of. They are so smart and always seem to find the one place you didn't think of.
My second youngest was eating her bedding too when I first got her. She has quit doing that as she found out that hay was much better than bedding.
Only 1 of my 4 girls is spayed. I don't think your babies will change that much after they are spayed and neutered. Their personalities are their own, no matter what. It won't change who they are completely, just merely calm them down a bit (sometimes not at all as I have found). So, I don't think they will lose who they are. They will just become calmer less aggressive versions of themselves.
As for adding the third rabbit.... I have four wonderful angels... I would love more; but, just don't have the time with the work thing always getting in the way. I think your thinking of the third is a great idea. I started with two and one died suddenly (very sad). Then I got another to fill the void for my single female. After a botched bonding I separated them and ended up with four. So, having three might be the best plan. Besides who can resist another little face and soft little body?