The in and out of the box thing may simply be that he still doesn't entirely trust that he'll be able to pee without pain. If that's the reason, it should fade with time.)Charlie did have some decent pee today, still not HUGE clumps but bigger than nail size. He did the whole 'in and out' of his box thing for a bit again, which of course worries me when he does but he still released a good amount of urine, I think.
But with so much good news, we're going to relax (which will help HIM relax), focus on the good stuff, and see how that goes!