Ah yes... the joys of vehicles and rodent infestations. I deal with this on an annual basis at work. Well, let's start with the easy stuff:
~While you have the blower motor out, get a flashlight and a small mirror (or if you have a borescope use that instead) and get the mirror position in the blower housing so you can see into the Evaporator Core. You're looking for any signs of nesting/debris/feces/urine/etc. that indicates the rodents bypassed the Cabin Air Filter and moved into the HVAC box.
-IF they have done that, you're going to probably want to pull the HVAC box and determine if it's cleanable, sometimes they are. (Note- We have had hit & miss luck with cleaning out HVAC assemblies. The plastic that these things are made out of seems to be rather porous and while you might get the death/rodent stench out, it may just absorb the bleach/cleaner smell. As a result at work due to come-backs and such, we just replace the entire units rather than take the chance it comes back with the customer complaining that the chemical smell won't go away) I would also suggest moving onto the next inspection step.
-IF NOT then vacuum/wipe down everything really well and then install a rodent screen (I show how I did mine in my build thread:
Zombie Truck 2.0 MPAV Build!) and call it a day. Realistically speaking, there are other ways a rodent could theoretically get inside the vehicle besides the HVAC inlet (the most obvious being if you're leaving your windows down and the vehicle unattended for a while), but I haven't really seen any of our customers have reoccurrences after we've installed a screen. It seems to be enough of a deterrent to our little furry friends.
~ Assuming you found evidence that they have gotten past the cabin air filter and into the HVAC System and/or vehicle I would check the following places:
-Pull the edges of the carpeting in the front footwells of the vehicle (along the door sill & towards the firewall where the wire harnesses for the doors pass through/connect is the usual place to look). Also check under your rear seats and the edges of the carpeting under the door sills of the 2nd row seating area.
-Also inspect the carpeting and spare tire tool storage area in the rear cargo area (pop off the covers for the tail light bulbs and see if you can see any nesting/evidence of rodent intrusion behind the panels.
-Finally (or do this first if you're flat rate, lol), pull the top edges of the door sill weather stripping off and gently pull down on the headliner itself. You don't need to pull too hard, just enough that you can get a look at the back side of it along the doorsill to look for any signs of nesting/feces/urine stains/etc.
IF you see any evidence of rodent droppings/urine stains/nesting/etc. in any of sections listed above, the interior of the vehicle needs to be removes and further inspection of rodent damage will be required. I will also add that in my experience, if they've gotten all the way up into the headliner; then they've been everywhere else in the vehicle already. It always seems to be the last place they end up after they've had their run of the vehicle. This is usually something that you'll have to get your insurance involved with and with older vehicle it can end up totaling them outright after tearing down and finding thousands if not tens of thousands of dollars of damage. That being said, the use car market is insane right now, so the value of the vehicle will likely be in your favor in that regard.
Post Note-
You can also play the "Ignorance is Bliss" card and just clean the blower housing up and install a rodent screen and hope you never have to acknowledge the possibility they may have gotten further into the vehicle. If you're not having issues with smells/stains/etc. after you clean the blower motor... it may be best to just not open that potential can of worms? I know a lot of customers don't seem to care/notice the rodent infestation until there's a rotting corpse (seriously... you have no idea how many dog owners and old people just seem to be oblivious to the stench/signs that their vehicle is just totally infested with rodents; like I can open the door and I already know that vehicle needs to be torn down... BLECH!) and a lot of times even
IF they did make a nest somewhere else in the vehicle, if it's not causing problems; once you prevent them from getting in, you should be fine.
