I've had MS for 23 yrs now and I've never had cracking jonts. As funny as this might sound I had a horse (before the bad tines) that had cracking snapping sounds coming from her feet and ankles when I purchased her. Fearing the worst I called our vet who examined the horse and said she was fit as a fiddlw but hadn't had enough exercise with the previous owner and she just had air trapped between the ligaments and cartilage. After 3 months of riding 6 days a week from 9-3 I never again heard any sound coming from her joints.
I don't want to make light of your problem but I was wondering if humans might not have the same thing?