[lowtops]

Florida,
I have a 91 and have spent way to much time looking at the engine bay trying to figure out a way to mount a battery in the engine compartment. You are on the right track. A small battery, an optima maybe, would fit beside the master cylinder but you would have to fab a holder for it. On mine there are even places for bolts on top of the inner fender well. The other option would be to move the air injection system beside the master cylinder and use a battery box from an FZJ80. I think the second option would look more factory but I don't know how hard it would be to move the air injection system. If not done properly it might throw an EGR or some other code. I have contemplated totally removing the fan and black tube (see last pic. on the right hand side in your post) that blows air on the exhaust. I'm not really sure how much good that fan does anyway. Plus I have never seen mine actually working. Maybe someone else can shed some light on the function of that fan.
If you come up with something do a write up on it, because as you said there is not much information on this subject using the search function.
Raven makes a good point about using the 62 as a model. A search in the 62 section might shed some more light on the subject. I haven't thought of that before.

Good Luck