Flights to Mazatlan - JFK to MZT

[dalefried]

I need some help here, and I am hoping that my faithful frequent travelers on this site can help me. My husband and I are traveling to Mazatlan from NYC. There are not too many flights from JFK to Mazatlan. Right now US Air has the best itinerary and the cheapest price. Here's my dilemma:
There is only 1 flight that leaves in the morning at 6:43 a.m. from JFK and arrives in Phoenix at 9:11 a.m.
- There is a connection to Mazatlan that leaves from Phoenix at 10:08 a.m. and arrives in Mazatlan at 1:17 pm. The plane is an Airbus. The layover is only 57 minutes.
- There is another connection to Mazatlan that leaves Phoenix at 12:00 pm and arrives in Mazatlan at 3:06 pm. The plane is a Canadair Regional jet. The layover is 2 hours, 49 minutes.

My first inclination is to choose the first flight since it is the shortest duration, but what happens if the morning flight from JFK doesn't arrive on time, and we miss the first connecting flight to Mazatlan? Would I be able to get on the later flight to Mazatlan? It is a much smaller plane and may not have available seats. Or should I choose the 12pm flight to be safe? What happens if my flight from JFK to Phoenix gets in on time to catch the earlier connection? Could I go to the Gate and ask to get on the Standby List? If my husband and I are allowed to get on the earlier connection, what happens to our checked luggage? Would it be transferred to the earlier flight or would we have to wait at the Mazatlan Airport for our luggage to arrive on the later flight?
I want to purchase the tickets soon because of the lack of flight choices to Mazatlan. Thanks.