Wow! All those allergies, poor girl. Bless your heart for taking care of her!
I agree with dray, sounds like she may get some relief with immune boosters, supplements, vitamins, something. It may not totally "cure" her, but surly there's something out there that will help her some.
Have you tried a litter box on your covered porch? Kitty litter or the stuff they make for doggie litter boxes or even just plain sand that could be replaced as it's used.
There are several brands/types of doggy boots that should go on pretty quick and easy. Even if the initial cost is a bit, they'd last for a long time and are designed for dogs so fit shouldn't be an issue.
Gosh, what a dilemma, please keep us posted with what you try and the outcome.