I don't really think Mexico is all that Sketchy, at least compared to parts of the USA. Common sense rules apply everywhere.
You can see a lot of Baja without leaving pavement, so when people mention that you have to go offroad to see the best parts don't sweat over it. Temperatures varied alot from one coast to the other when I was there in Aug/Sept, and I expect that will still be the case. You're going to be there at the right time to go whale watching, but I can't recommend a boat.
There are a couple sea turtle sanctuaries along both coasts, and I camped near one on the Sea of Cortez side. It was an interesting stop, but I was too busy having fun to take notes and Google wasn't helpful. Some one will probably chime in.
To get to the mainland there is a ferry from La Paz. I went to Mazatlan, and shared a cabin. You don't need a cabin, but it saved me having to find deck space to sleep on. I also recommend the inland route, through Morelia and Oaxaca rather than along the coast. It's a lot less touristy and the food is better.
I crossed into Guatemala at La Mesilla, which was the lowest-stress border crossing I think I have ever had. This is north of the Pan Am, and takes you to HueHue. From there you should be able to reach the north, and from there to Belize. Obviously Tikal should be on your list of places to see, but there are other smaller Mayan sites up there if you don't like crowds.
I didn't go to Belize, so I don't have any advice there. My understanding is that it's all amazing, though.