I'll pitch in.
I sure hope you can afford to keep this thing for many years and have the time, patience, and cash to make it exactly what you want. Research the look you want and try and decide how you think you will end up using it. Daily driver? Rock crawler? Both? That's for down the road.
For now, I would look for any and all rust that will ruin your day later on. There are lots of common places on the FJ40s that they all will tend to rust in. Here's the first round for a beginner to look at.
A) Across the bottom of the front bib. See if the bottom side of it is flat all the way across or if it is bowed downward. It's two layers of sheet metal and dirt and water love to collect in there and rust it out.
B) Right where that mess is on the fender. The fender brace is under that portion of the fender and it's also a collector of the enemy.
C) Looks like you have this one too. Easy to see from the underside. It's self explanatory.
D) Another seem that harbors crap. Looks like the waves in the paint are covering up either the beginnings of rust or bondo from an attempted fix.
E) right behind where that cool little reflector is there are layers of metal that once again are harbingers of death.
F) if there was one... All the way across under the ambulance doors.
There are metal guys on here that could give you the best way to handle these without coughing up all your money fixing them right off the bat. Look to them for advice as to keeping it from spreading until you can repair it.
Good luck!