ServiceAward, it sounds like you're doing everything right. The thing I would caution you to be aware of if they subcontract the job out.
With the electrical, most municipalites want a licensed electrician to at least bid the job. Doesnt mean they will be doing the work. In my experience electrical needs a permit unless, as mentioned above, it's installing a new switch or outlet inside where nobody sees. But not a complete rewire of your garage.
IMHO, if the contractor was shady and knew how to do it, he would have accepted the rewire no permit and go for it. This guy seems genuinely concerned about loosing his contractor license. Just my opinion.
If you live where hurricane ties are needed you might ask how much of an add on it would be to add to the other joists. Or if its exposed rafters to the walls DIY. if its between the rafters and the sheething, nevermind I brought it up