M & M..what's a mom to do?

So long before we had little Beaner, we had Maya and Molly. Our kitties. For a long time these were our children..hairy, messy and they fight with each other. Typical children. But now I have a dilemia as a mommy. As many of you know, we moved into our first home last January. It's a great house and we are taking a lot of pride in fixing it up and making it ours, starting with new carpet. We are getting the downstairs done to serve as our main living room/romper room area. Upstairs we need to get our computer room done because the previous owners had naughty kitties that peed on the carpet. Subsequently it is right by my desk where I work on my computer so I complain about it... ALOT to Matt. Anyway.. Our kitties have had some issues. We got Molly to keep Maya company. Yeah. That didn't work out too well. They get along most of the time but there is that whole who is the 'top cat' thing that they haven't quite worked out yet. Maya just hisses and goes on her way but Molly pees 'inappropriately'. In our apartment, space was an issue for them so it was happening much more frequently. Since being in the house it has only happened 2-3 times but it happens on the carpet downstairs. Yes, the carpet we are going to replace! I am not happy with this obviously. But what makes me more unhappy is that it is a behavior issue between them and not something I can fix. It has been going on for 2 years now and they haven't worked it out. And if you know anything about cats, which I know WAY too much about, it probably won't by now. My thought is that Molly would be much happier in a 1 cat household. We made a mistake in thinking that these two adults cats could live happily ever after. My fear is that we spend all this money to replace carpet that has been ruined by cat pee only to have it done again. It is not a situation in which we are training a puppy and she made a mistake on the carpet. So my thought is to give her to a happy home. I don't want to take her to a shelter as she might be put down if she is not adopted. It hurts to think about and something that Matt is not happy about but I think I need to be the bad guy here for the sake of everyone. Does anyone know anyone who has had a similar situation or is open to welcoming a beautiful, loving kitty into their home? I really, truly hate that we are in this situation. She is such a little buddy. The next question I have is how do you know which one to give to a foster home? Ugh. It has all just become too much to maintain with Ella and work and our shedules...This sucks...

(Maya is on the top shelf in the picture and Molly is on the bottom.)