I’m thinking it might be a good idea to explain your set up.  I don’t have time to do much cleaning, so I’ve really established a system for keeping everything neat & tidy.

I line my cage in wee-wee pads.  They don’t chew, so it helps to protect the various linings or floors.  I have rag rugs on the shelf.  I vacuum them regularly, however when they need a more thorough cleaning I wash them in the machine.  I also line my litterboxes w/ newspaper.  That way I can toss the newspaper when I clean the litterboxes. 

I believe the staining is due to the amonia levels in pee.  Amonia can be used as a cleaning product, so that’s why it has a bleaching type effect.  Maybe some of these things would help out.

I generally always use vinegar, like you are using, for any pee marks. Does the pee leave the residue even after you use the vinegar to clean it? I think for the time being, a good scrub down is a good idea. Are you working on litter training Phoebe? Once she is litter trained then you won’t have to worry about scrubbing everything down so often, but for the time being, I think its the best idea.

I don’t really think there’s any safe cleaning products that are strong enough. I just buy a new litterbox every year or so

I soak my litterboxes in pure vinegar for about 15-20 minutes to soften the residue and scrub it out about once every 3 weeks. A diluted solution with help with some of the staining but it will still build up. I would recommend scheduling a once a month immersion in pure vingegar and scrub. I have not used anything else.