Looks like you had the time of your life, I'm happy for you. I've (recently) spent a year of my life down there (in the town of La Paz) and its one of the most amazing regions of the earth, truly. I had the old XJ down there and really put it to use. People down there have such a different attitude to "off-highway transportation." Its not viewed in such a negative light like it is here people don't start that bull* down there. Theres exceptions but property owners usually don't care so long as you stay on a trail and don't mess it up, I stopped at some ranchos before and offered up a box of powdered doughnuts or cold cokes and thats appreciated. Theres also a general attitude down there that beach access is an inalienable right, property owners aren't supposed to block it.
Anyway, I diddn't do any long distance travel like you did but I did explore a lot of remote places like beaches and mountains. I did visit that same mission. The thing about doing this is in Baja is that when you want to offroad to a specific destination there are 15 different trails that go off every direction soon as you leave the highway and 14 of them go nowhere interesting so its easy to get lost. I was living, working and taking classes there so I was lucky, I had local friends to show me where places are but otherwise its super easy to get lost. I recommend meeting up with a local or going in a group with someone that has been where you want to go before. Also if you like fishing or diving or any watersports its a world class destination.
The Baja 1000 race is pretty amazing. Heres why: the race is usually run in apx. 15-19 hrs, thats on rough offroad trails. It takes 22 hrs. to go the same route- on the bus- which runs on the paved highway. I watched some of it live in 2004, I wasn't too impressed just a bunch of buggies going by and a whole lot of dust. Actually driving the course sounds like a whole lot of fun though.
Anyway, if you want to take a trip to Baja California Sur, do it soon. Though the natural splendor and wide open beaches are 99.9% undeveloped, its changing REALLY FAST. Cabo, when I arrived down there was still a little village with a few hotels. A couple years later now and in comparison its a full-fledged city that would make California urban sprawl look quaint. The remote, scenic southern half of the peninsula is rapidly joining the 21st century. The place is really poised to change, probably not for the better when these areas aren't so difficult to access. Its still a huge, remote area but I feel that is isin't the same now as even 2 years ago so if you have a Jeep, head south, get on Mexico Highway One and take it all the way down, to the end of the peninsula. Just don't go in the summer because its so damn HOT the devil couldn't stand the midday heat.
Let me know if you want information about a specific place down there or want to see pictures on seperate thread. I hope you enjoyed your trip Alex (my name too) you got to see what I think is the better part of one of the most unique regions of the earth and have your own off-road racing adventrue doing it.