I am going through something similar with my kitty Chilli. Fortunately the last tests showed that the cystitis has cleared up (at the moment we have no reason to think it is recurring), but unfortuantely we now know that the urinating in the wrong places is now a behavioural issue (presumably resulting form the cystitis).
So far I am trying:
1. Feiliway plug ins.
2. Waterproof covers for sofas (e.g.
http://www.amazon.com/Innovative-Textil ... sofa+cover - available in the UK too)
3. Zykelene (for 2 weeks anyway).
4. Putting tin foil on the areas she is doing this on more frequently like the sofa and one of the DVD players (!!!).
5. Putting her in the litter tray (after removing the flap as I have covered trays) and comforting her and soothing her whilst she is in there. She makes it very clear when she has no need to wee but also clear when she does need to go. I then give her some treats once she is out of the box and praise her for being a "good girl".
6. Locking her out of the lounge, study and spare room so that she can't have accidents in there.
7. Using "Urine-off" when she does go (not that I think it is very effective).
As we only had the clear uring sample a week ago 3 and 5 are at very early stages and I cannot say that I have "cured" her yet but I am ever hopeful. There has been some success already with 5 as she has "performed" for me at times where I could tell she was about to go somewhere else instead i.e. she was crouched to go on the duvet and I moved her to the box in time.
Though, I would happily accept any advice on other things that I could do too!