All access points for animals and rodents have to be sealed or screened. Simply spraying a foam substance in a hole is insufficient. The rats will eat their way through it no time. If the skirting is loose and offers many points of access you can either have the skirting replaced, (not cheap) or line the entire skirting inside the crawl with a wire screen and attach it to the skirting. This is the most effective way to deter rodents from reentering your crawl space.
Once the access points are blocked the crawl space can be restored to a fresh clean environment. It is important that once the insulation has been replaced that a new belly wrap is installed correctly. This is usually a 12 mil polyethylene plastic that attaches to the floor joists and must be glued to entire perimeter so that it is completely sealed. This is another deterrent for rodents.