Oh gosh, so very sorry to read of her difficult history - I know exactly how this feels too, with my late Wylie
-- it's tough and complicated.
I would most def get a urinalysis asap, and see if there is protein in the urine - if yes, the vet will likely want to run a UCP.
As far as enzymes and probiotic - hard to say if this could help, but it does with some dogs - especially those who've had their GI flora messed up by some infection or whatnot.
Have you yet tried Royal Canin Hydrolized Protein? It really may be worth trying.
Has an ultrasound of her abdomen ever been done?