You definitely have three zones, based on six control pins between 4 and 6 AM (three pins turn the system ON, the other three turn it OFF).
You also have an indexing valve (so you will want to update not only the controller), I've been in similar situation (link), upgrade is well worth it.
For example I see that your controller is set to water one of the zones for twice the time of the others, but if there ever been an issue (which is very likely) whereas power went out (due to Florida hurricanes) or something similar, in a middle of the cycle, your controller would go out of sync and from than on a wrong zone would get twice the water.
It took me about two days to replace a similar timer and four zone indexing valve, professionals can do it in a few hours. Adding a motor relay is pretty straight forward, you can pick one up in your local Home Depot or Lowes and wire it up to the master (M) terminal (don't forget to enable it in the software).
I'm also in Florida, water savings and rain awareness are well worth it.