What happened to our good kitty?

In May of 1998, I found three kittens under a tarp on my patio. They were no more than a few days old! It broke my heart seeing them lying there helpless and abandoned by their mother. My girlfriend and I took them to the vet to have them checked-out and to get instructions on how to care for them. Unfortunately, one of them didn't survive. The other two thrived under our care. I did most of the feeding (using a big plastic syringe) and both the kittens really seemed to take a liking to me.
As time went on, one cat (Booger) just fell in love with my girlfriend. Booger still liked my attention, but there was no doubt that she was really attached to my girlfriend. The other cat (Mr. Brain...we thought the she was a he when we named her!) just didn't seem to like my girlfriend very much; but she was really attached to me.
Well, to make this long story short, my girlfriend and I split up about nine months ago. Since these two cats had been together all their lives (they've been spayed and have always been kept indoors and we didn't have any other pets) I didn't like the idea of Booger living with her and Mr. Brain staying with me. It broke my heart to see the kitties go, but I thought this would be the best thing to do.
Everything seemed to be going well for them until about a month ago. My ex-girlfriend (we still stay in touch; I've gone over to see the kitties every couple of months...) tells me that Mr. Brain is not using the litter box and is making a mess of her place. She also says that they fight all the time now; they never fought when we were all together.
This really surprises me for two reasons: I would have expected this to happen shortly after they moved to the new place; not eight months later! Also, both of these kitties have NEVER done anything like this before. They truly were GOOD kitties and a joy to have around. They were both taken to the vet and she found nothing wrong with them (this included blood and urine tests).
My girlfriend wants me to take Mr. Brain back, and I don't have a problem with that. Actually, I like the idea, but I have a few questions that I hope someone can help me with.
First, what can I do to get Mr. Brain to use the litter box when she comes to live with me? I've read some of the other threads, and I plan on getting a new litter box and putting it where it was when she lived here before. Is there anything else I should/could do?
Is my thought that keeping them together is better for them? I thought that was the best thing to do, now I'm not so sure.
Also, I recently purchased some very expensive leather furniture. I've been told by more than one person that cats and leather are not a good combination. Is there any truth to this? I am determined to give Mr. Brain a good home, but if she destroys my new furniture (she is de-clawed, but I'm concerned about her soiling it) I will not be very happy. I don't like the idea of keeping her shut in a room all day while I'm at work. I never had to do that before, and I don't want to have to do it now.
I need some help on how I can make this a smooth transition. There is absolutely NO WAY that I would consider euthanasia. I raised her from a little baby and I have to admit that I'm pretty attached to her. As for the breed, she is an American shorthair; although Mr. Brain has some pretty long hair!
Sorry for the length of this, but I wanted everyone to understand the whole story.
I appreciate any suggestions.

Thanks, John

Unfortunatly after a cat has it's claws removed there are some behavioral problems. #1 being going outside the litter box. It hurts them once litter has made it's way into their now cavities where their claws were. As for splitting them up, if they are fighting I would definatley bring her back to live with you. If you do this, I would first put her in a small room like a bathroom by herself. I would get a litter that will not harm her feet such as the crystals or pine litter. Somthing big enough not to get into those cavities. I would make sure she is using the box on all the time for at least a week and if she is, I would let her out to explore. As a very serious cat lover I personally would not be too worried about the furniture. It can be cleaned and leather is much easier than regular fabrics I might add. If you take the time with her you can get to the bottom of what it bothering her. It may be the litter, it could be something your ex did, it could be something that happened between the two cats. There are so many things, but I would start with what I told you.

Thank you for your reply Sandie, I appreciate it.

One thing I would like to add: they were both de-clawed when they were young (probably two and a half years ago). Neither of them had any problems. That's why I'm puzzled by her change in behavior.
I also agree that worrying about the furniture is a non-issue. But I would prefer to avoid that problem if possible.
Thank you again for your help.

John

Just keep in mind that time has no bearing on how they react with the loss of claws. Cats who have been declawed also tend to develope artheritis which may be causing some discomfort. I would still explore a softer litter for her.

What about no litter at all? Some people have good results with shredded newspaper, which certainly wouldn't clog her feet but she could still follow that instinct to bury. A stainless steel litter pan doesn't absorb odors and is virtually non-stick, so you would just need something to absorb the wetness. The cost of a metal pan seems high, but I have used one in the past with very good results. Plus it could be cleaned out with soap and hot water and was very sanitary.

For what it's worth, I had two male littermates for several years. We owned their mom so I'd had them from birth. Sparky was an energetic red tabby with a very affectionate and outgoing personality (hey, he was named that for a reason); Blackie was more mellow and often seemed to defer to his brother. For about 3 years they were very happy together. Then we went away for a week, and when we came back Sparky actually woke us up at 3 or 4 a.m. with his wailing to go out. We figured that, after a week of being cooped up, he wanted out in his yard. We let him out and he took off, and didn't come home. We never saw him again, although some neighbors who had a dog claimed to have spotted him with a different family on their walks.

Once Sparky was gone, Blackie (who is still with us) really opened up and bonded with us. I have wondered if he didn't somehow drive off his brother, after years of sort of being in his shadow. Perhaps they had some kind of competition for "alpha cat" and Sparky lost. Maybe Sparky just preferred the other people. So I don't know what happened between them, but I think sometimes littermates just need to get away from each other.