If the dry stack is in good shape, I don't recommend messing with it except to fix any slope / drainage issues around it - if it isn't you need to get a stone mason to look at it.
This is a case where it is best to handle the issues from the inside, generally with infloor drainage, dimpled drainage mat, and closed cell foam. I am assuming you are looking at going with a sealed crawl space seeing you mentioned the foam
As for the critters I am going to cheat & point you to an article I did on keeping squirrel's mice & raccoons out of the house
Hi John, John, and Sean,
Once the structural issues as Sean mentions are out of the way I have suggested in the past that the inside be sprayed or hand mortared to fill all of the gaps so that the critters will not find a soft foam filled way to regain their access. Foam applied from the inside does look nice, but would not be effective on critters, at least the ones I have had to deal with.
As for cost, a mason would not take that long, especially if the surface was going to be covered with foam. If the pool guys were not bust, they spray pools in a similar fashion and perhaps their material would be suitable. Stucco applications might also be worth considering depending upon your area. So, whether it is by hand or machine, an inch or two of mortar in those gaps should work well to eliminate the unwanted guests.
My 1850's Greek Revival has a dry stone foundation. I sprayed the inside from the floor to the top of the rim joist with 2.5" (R-15.5) of closed cell foam but did nothing to the outside (granted, the dry stone foundation was only below grade but had granite foundation stones above it). After two winters, there is no sign whatsoever of rodent entry, whereas before they were all over the place. It appears they don't like the stuff. The foam was ComfortFoam from BASF covered with a code-required flame retardant paint. Total cost: $5665 for a 2862 sqft house (sorry, I don't have the square feet of foundation area).