You could see every seem and every sheetrock screw under the paint because they were black from the 'filtration soiling'.If there are patterns that reflect any seems or fasteners, this would be my guess... in which case a good coat of paint would help seal it. 

I personally went in and saw visible ceiling water damage and atleast one window that was not sealed properly (Large air gaps).

Problem is, if they did that they all but sealed their fate to get NO equity at all.

I've talked with several contractors about potentially jacking up the roof and replacing the beams, demoing the roof and rebuilding, and even filling the whole garage with dirt and sealing it up, but my usual crews aren't interested in tackling the challenge. 

Try to find a local exterminator that doesn't have a fancy car and a big ad in the phone book.Those kinds can rip you off with high fees.There is a difference between pest control and exterminating.I can tell you ongoing pest control is crazy for what they charge.With mice you just do not want to plug up a wall.They will come out in other places in the unit or if they can't get out will die in the walls and stink up the place.The tenants just as with squirrels will complain they scratching and moving in the walls keeping them from sleeping.Also they can chew on electrical behind the walls and cause problems.You have to make sure the unit is clean and stove is clean.Then you have to make sure you have no breeding grounds or trash outside of the property.Also you have to make sure property is sealed well from the outside so they can't get into the small openings.Paying for an exterminator won't help if you don't seal the outside and fix the inside.They will just get rid of a few mice and you will have more again.

In really bad cases, you have to remove the carpet and the padding and seal the subfloor before you can put new flooring in.

The upper could be sealed off from the bottom and an exterior stairway added and likely get $400 for the upper after being rehabbed.Thoughts?

The inspector will require some type of documentation that has the engineers seal and signature on it, which is why they are licenses. 

The house also has a couple coroner seals on two of the doors, so I will also need to consult with them, as well. 

My fear is that the former will recommend a bunch of smoke remediation (sealing, etc.) that is no longer an issue.