Awww,what a little sweetheart
you obviously love her very much..
To be honest,I would not worry too much about paws having been in the litter,cats are keeping themselves very clean.
I often kiss the soft little pads on my cats paws,only when they are sleeping though..and they are pretty well allowed to go wherever they want,or are able to,since they are 14 and 9 yrs old.
I hope you do not have any plans of de-clawing her when her spay-time comes.
Some vets(my old one did)will suggest de-clawing when they are going for a spay,please don't,it is horrible,no matter what the vet says
As for getting her used to a harness,that's a great idea,she will squirm at first and maybe even get out of it,you could get her used to it in the house,but only when you are there to check on her,so there are no accidents.