Should I redo the brake cyls and calipers? Should I consider the 4Runner calipers up front, or even rear disks? Seems like a lot of work on a system that really isn't that bad in the first place...
You have answered your own question
• What sort of method/trouble can I expect from stripping the paint to the bare metal? I figure I'd do it in sections, not all at once - and I probably won't remove the glass or the inside junk (door jams, etc) - also, what wheeling I do is usually expedition stuff, and I wind up scratching the hell out of my paint (trees) - should that have any bearing on my decission to paint/LineX? - I only wheel it maybe once a month...
That kind of effort is for custom rodders who want a perfect candy apple red paintjob to win trophies
Not for occasional expedition rigs.
It takes a lot of work for not much gain stripping them back to bare metal.
• I'm thinking about the CS144 GM alt upgrade. Would that do it, or should I consider dual batts, also? I'm not expecting to run a winch or a thumping sound system - I just want to run what I've got reliably.
Why not find out whats wrong with the one you got 1st. It maybe resistance from corrosion in the wiring. Pretty common at your cruisers age
• Should I mess with the rear axle at all, even though it seems to be fine? (bearings, seals, etc?
You have answered your own question again

Why torture yourself over a highway come occasional expedition rig.
• I don't know what shape my rear springs are in - they're partially held up by those crappy coil/shock combo things...are OEM rear springs available? I may put a bull bar upfront, too - if I do, can I keep my factory springs? I don't want to do an OME susp. lift or anything. can I get away with an addd-a-leaf?
Get some new springs. Even a highway rig benefits from good springs.
Dont waste anymore $$$ on patch up crap like add a leaf.
"Any other suggestions on what else to mess with? Do I seem like I'm on the right track?"
Prioritise!! Get all the things that make it a pita to drive fixed 1st.
The time and effort spent stripping paint back to bare metal is better spent on the suspension and other mechanicals.