Just came upon your ride report. Thank you for the time and effort you are putting into this. I rode Baja to La Paz to Mazatlan earlier this year. Had no trouble at all with getting a TVIP in La Paz. I didn't even have the original of my registration only a copy and Mexican law says you have to have the original. At first they said I would need to get the original but after a while called me back and said they would accept the copy. I did have a problem getting the total cash amount I needed to pay for documents + Ferry fare etc. out of the bank, they had a pretty low daily total amount you could take out. I was able to work it out with a manger.
I have visited Mazatlan many times since 1985 have never had trouble at all. Do not speak Spanish. I think the Mexican people are some of the most helpful people I have met and a little mutual respect and taking things easy goes a long way. Things are done differently and at a different pace, accept that and life is a lot easier.
Relax, ride safe and enjoy your trip.