Arriving in Mexico you will have to go through passport control, baggage claim (if you have any checked bags) and customs - so depending upon day and time of arrival this can be anywhere from 30 minutes to 1.5hrs plus. I would allow at least 2 hours connection time arriving from the US to allow for any delays on the incoming flight and delays in processing on arrival.

SJD and PVR are pretty small airports so while I have not personally been to them I suspect making it will not take long in terms of physically getting one gate to another. However, you will almost assuredly be required to leave the sterile area to check-in w Air Alaska for the return to USA. I have no idea how efficient Air Alaska is at that station. You might or might not then need to go through exit passport control where you turn in the FMM card (if one was given to you on arrival in Mexico - Mexico seems to be in a transition away from the card but at different stages of this at different airports). After passport control (if needed) you will then go through security. Then to the gate where there might or might not be additional security screening. All of which is to say, I would plan at least 2.5 hours connection time to the return flight to USA. Your incoming flights could well be delayed....

How much time you allow for connections all depends on how critical it is for you to make the connections.