Birds bathroom vent mess

Wheats

A few weeks ago I noticed a "bird cage smell" in my basement bathroom and a birds nest(sparrows or swallows) in the vent on the exterior wall of to my finished basement bathroom. The 4" vent pipe extends 8 feet from the bathroom, through the ceiling between the joists in the hallway ceiling out to the exterior. Knowing a blocked vent is not good I went up there from the outside and cleaned the nest out to discover, being the Columbo-like investigative homeowner I am, more to the story.

The genius who put in the vent must have run out of foil-like flex pipe and finished the last 4 feet with plastic dryer vent pipe. So birds had broken though the plastic and made nests in between the joists, on the drywall in the ceiling, and packed some of the foil-like vent pipe with nesting material . I cleaned out as much as a could through the 4 inch hole (enough to fill a 10 gallon bag!). The bird cage smell remained. So I went a little further and took out the drywall ceiling inside to expose/replace the pipe at the hallway closest to the exterior wall. Removing what appeared to be years of nesting and oh yeah many unhatched eggs, I am wondering if I need to do any disinfecting,and how, before I replace the ceiling? Also, Just past the hallway ceiling where the vent pipe drops into the soffit area above the tiled shower tub leading past to the fan in the middle of the bathroom I can see with a camera (but cant reach) some bird droppings on that ceiling material but dont want to rip out the tiled ceiling in the tub to clean it. What are the issues if I can't clean up all the droppings? I have already purchased 8 feet of flexible metal duct, foil tape, a new vent, with rodent/bird guard to replace the damaged area. Any suggestions and tips would be helpful. Also, note since cleaning out all the bird material and dry vacuuming the area the bird cage smell has gone, thank God!