Bloody Urine in Bad Places

So,  Bella is the most beautiful feathery white cat and has proven to be a wonderful companion.  She had a bit of a rough time because I moved across the country twice in 6 months.  I also volunteer a lot at the Humane Society in my county so I have ended up adding two animals to our household in a year.  She didn't start the bad peeing until I moved across the country the second time.  I think that was what put her over the edge.  Oh, and she is deaf and has been since she was a kitten.  This makes it very easy for our 7 month old puppy to sneak up on her.  He is never mean, but sometimes she doesn't want to be played with.

She is a high strung animal as evidenced by her behavior every time she goes to the vet.  She is fine when I am there, then apparently she flips out as soon as I am gone. 

Bella pees in bad places.  Anytime there is a bag on the counter, a box, towels on the floor while I am sorting laundry or my bed.  She has to be restricted from certain rooms in my house.  There is always blood in the urine and it is always a small amount.  When I catch her at it, she never appears to be in any paid.  She is very matter of fact about the whole process. 

We have been to the vet many times to try to figure this out.  She gets bladder stones which I know are painful especially when she has to pass one.  I have never noticed her showing any signs that she is in pain though.  She is on medication that helps keep the stones from forming and it is also an anti-anxiety medication.

She is on the medication and I make sure to keep the litter box very clean and she still pees.  It is getting to the point where she is ruining big items in our home (furniture, mattresses, etc)  I am starting to wonder if I need to resort to getting a cage for her (one of those big ones that you see at the Humane Soceity with the 2 levels)

.  She is good in every other way.  She is totally sweet to visitors and to us.  Has never acted skittish or anything.  She is very friendly, but she is runing our house.  I would never get to the point of getting rid of her unless I found out that she was in constant pain and had to deal with that.  I owe her a lot.  She was my only companion when I was in a new city and didn't know anyone.  Every day when I came home, she would run down the stairs to greet me as soon as she saw me turn the light on. 

I don't like the idea of putting her in a cage.  She is very curious and active and would be miserable.  I don't know what else to do. 

Is there a way to recondition her to not pee in bad places?  Is this a result of stress and maybe more medication would help?  She uses the litterbox too so it isn't that she doesn't know any better.  Any advice would be appreciated.