You are powerless to remove the tenant while the courts are closed and there is a stay at home order.

In any case, I found the following after she moved out:- Smoke/animal smell throughout the unit (she was a smoker and smoking in the unit was strictly prohibited and dog was allowed per the lease)- Carpet with cigarette burns and soaking wet at the time of removal (no telling how long its been like this)- Rear window has a broken pane (still functional as it is a double pane, but needs to be replaced regardless)- Holes in drywall- Replaced bedroom doorknob with deadbolt (because her middle school son was stealing cigarettes lol)- Backyard full of metal/wood fragments and general rubbish including shoes, a knife, batteries, fishing reels etc. 

What are the typical costs of removing it?

If there's any question, I would wash it, seal it, cover it with 6 mil plastic and then go down with the new carpet and padding.Spraying/drying does not "remove" anything.

Lower unit: new floors, texture and paint walls, new light and plumbing fixtures, new doorsUpper unit: making a larger kitchen with an open concept living dining and kitchen, new floors, rock, tape and paint throughout, new trim and doors, new cabinets and new bathroom New windows and siding, 12x12 decorative concrete patio for each unit, new concrete floor in garage, new driveway, removing elec baseboard heat and putting naturally gas forced air in both units.

She says they have been there for 6 weeks, which I knew was a lie because I had just been there the day before but this lie was concerning because in Vermont if you have occupied a unit for more than 28 days you are considered a tenant and I was concerned the police wouldn't remove her and tell me I had to go through an eviction process.

That would remove the bulk of your risk and put some cash in your pocket for the next local transaction. 

We removed a couple of walls for an open concept and add an island.

Now fast forward to today two months later, the lender just said my husband has to be on the title and the deed as well, and I can do a quitclaim after closing to remove him.

The seller has now tried to inform us that he will not provide needed documentation to the title company as a way to avoid him having to remove the tenants while we are in the closing process.