Is $2,000 to humanely extract birds and replace damaged siding a fair price?

I noticed feathers and tiny caterpillars blowing up through the vent in my child’s room. I knew we had birds inhabiting the perimeter of our house but did not know the extent and did not know they had actually pecked their way INTO our air ducts. They got in through the vents on the side of our house. We also had a piece of siding blow off that we thought was just cosmetic, but really, gave these birds access to our whole house. They’ve also been crapping in there. After the initial assessment and remediation, I'm finding it difficult to find a business that can properly clean and sanitize the biohazard in the ducts to the extent needed. The general consensus from companies is that our ducts will likely need to be replaced, which would require ripping out walls and ceilings for access. My insurance does not cover pests of any kind. I'm concerned about potential health risks, especially since a friend's child almost died from E. coli from bird poop. We are young, first-time homeowners and are learning. Previously, our furnace wouldn't light due to nests. We've heard them in the middle of our house in the ductwork, indicating they've gotten far in. I have 4 different companies coming next week for further assessment.