1. The toll booth take overs can change daily. They don't stop vehicles, just ask for donations.
2. There is one actual bypass for Navajoa, on the west side of the city. It is very easy, just watch your speed.
There is a Truck Route that runs parallel to the main through town road that is one block to the east of the main road. You pick it up right after you cross the bridge. You are required to take either the truck route or the bypass. Both are easy, actually easier than dealing with the lights on the main road.
3. Don't know, haven't heard anything lately.
4. The ins and out of getting vehicle permits with your temporary residency is up for discussion. You will get your paperwork at Nogales. If you already have your 10 year permit you need to do nothing with that. The car, you can get your permit on line ahead of time and save the stop, or you can do it in Nogales. It doesn't matter what state the car is licensed in as long as you have all the paperwork you need. You don't need to even mention the RV as long as you have the 10 year permit on it.
I think they shut down the facility at Empalme. Make some phone calls, and be sure. Otherwise you'll likely have to drive up to Nogales.
Good Luck, safe travels, keep us posted as to how it goes, and have a great time! Moderator