I would go back to your vet and ask for further checks, it does sound as though it could be cystitis. Cystitis isnt often caused by bacterial infection so the urine tests wouldnt necessarily show up anything untoward. Stress is a contributing factor as is feeding dry food only so, if its possible it could be cystitis, you could try plugging in Feliway diffusers and changing his diet (gradually) to wet food (with no cereals/grains etc)

I would also provide add another tray in another location, so he's always got one avaialbe wherever he happens to be, and maybe think about changing the type of litter you are using - cats generally like to use fine, sandy type litters rather than the larger granule ones.

To clean up the areas he's wee'd in, use a solution of biological washing powder and water to wash thoroughly, then when its dry, spray the area with surgical spirit so that he isnt attracted back to that spot.

But I think another check at the vets first.