She certainly sounds like she's improving and she's definitely in the best possible hands. MS doesn't always display any other symptoms than the hot swellings. Occasionally, birds go on to develop respiratory symptoms.
I'm *thinking* that birds with lots of recessive genes (more likely to be inbred and less genetic diversity) are more prone to infection than more genetically diverse chickens. I haven't found anything to back this up in the scientific papers but my course tutor agrees there's empirical evidence of this.
Your soil WILL contain e.coli as, as I'm sure you know, all soil does. The question is, is it proliferating excessively in your soil? The lime should certainly make conditions less favourable to any bacterium, virus etc.
You could try adding a gentle diuretic if you suspect kidney issues. I have used a custom blend available over here but you could just use a tincture of dandelion or moringia powder? Take a look at this on Poultry DVM:
Genetics - certain chicken breeds have been identified to have a simple autosomal recessive gene that causes a defect in the renal tubular secretion of urate.
See more at:
https://www.poultrydvm.com/condition/gout
Unfortunately there's no further information as to which spcific genes and breeds are disproportionately affected.
Does she like cherries? My dad suffered badly with gout and he swore by cherry juice! There have been studies where it has been found to be clinically effective.
Let me know how she's doing. I'll keep everything crossed for her.