Eek, that sounds like a lot of extra work! I'd estimate almost a whole extra month, maybe more. From what you've described, even finding out which clips belong to which scenes could be an exhaustive task. So either add to your quote quote accordingly, or ask the producer if he (or the script supervisor or director or anyone else who was on set or already involved in the production) can sort through the footage first and make it more approachable.

Foley sound is audio effects created in post-production, rather than recorded on set or taken from a licensed library. I believe the strange name comes from the name of the person who invented the technique. A Foley artist usually watches the film (or scenes) once they're edited in sequence and uses a whole collection of items to create sounds that match the imagery, such as footsteps, splashing water, doorknobs etc. Often the sound effects are created by objects that have no relationship to what we see on screen - hence the classic jokes like Monty Python's coconut horse-hooves, or the Simpsons "Cows don't look like cows on film".