Just for reference you could buy a 200R-4 from a place like California Performance Transmission for $1699. All in you for TQ convertor, shipping and various other parts anf install you would be at around $2500. Still well under his quote. Plus you would have an overdrive gear. I'm not recommending CPT, but do know a couple people who have had success with them.

His $3500 suggests that he thinks there is more wrong with the car beyond the trans. That and the "well one thing leads to another" comment.