Take a Benadryl or two, don a mask, goggles, and some palpating sleeves and get after it.

USE BEDDING. Pododermatitis is NOT fun, and neither is urine soaked fur and urine crusted tails. Rats NEED to be clean, if they aren't, it makes them neurotic because they can't get clean.

Use aspen or a low-dust bedding. You can screen it to remove even more dust. You can use pelleted recycled paper(Yesterday's News in the cat litter section).