Sounds like there are two parts to your question.
Look for rust in the rockers, above the rear wheel wells, in the floors along the rockers, and at the front body
mounts below the driver's and passenger's feet.
You'll probably want a dana 44 front axle with disk brakes, which started in mid '74 (before that, Scouts came
with a drum brake equipped dana 30). If you decide to go with an earlier Scout (like for emission law reasons),
swapping a '44 into a dana 30 equipped Scout is a bolt-on (make sure you swap the proportioning valve, and the
master cylinder would be a good idea too).
The 4 speed from '71 through '75 was the T18 with a 4:1 first gear. Starting in '76, Scouts had the T19 (full syncro)
in either a close ratio (4:1 first) or wide ratio (6.3:1 first). The close ratio seemed to be more common, but you can
swap a wide ratio in place of either a close-ratio T19 or a T18 easily. A Borg Warner (I think - anyone know for sure??)
automatic was available in the early 70's, and then they switched to the 727. If you want an automatic, I'd stick with
the 727 - there are lower gearsets available, and there are options for using some Jeep 727 parts to use other transfer
cases (Jeep dana 300, Atlas) that you won't have with the other auto - but again, swapping parts is pretty straigtforward.
Most Scouts came with a dana 20 transfer case with a 2:1 low range. The main exception to this is the 1980 Scout,
which came with a dana 300 (2.6:1 low range) - the dana 300 from a 1980 can be swapped in place of a dana 20, but
they run about $500 and up, since Jeep guys like to swap them in place of their dana 20s too. One other good thing
about the dana 300 is that Tera makes a 4:1 gearset that you can swap in (only works behind a 4 speed). If you buy
a dana 300, make sure to get the bull gear (the gear that bolts to the output shaft of the transmission), and make
sure to get one that matches your transmission type (T18/T19 vs 727) because they're different. I hear that some
Scouts came with a single speed chain driven transfer case (actuated by a knob on the dash instead of a lever) -
you might want to avoid these unless you plan to swap it out.
345 and 304 V8s, 258 (AMC) I6s, 196 I4s. Obviously, the 345 would be the most desireable for off-roading, though
the 304 isn't far behind in low-end torque, and they are bolt compatible (as well as being bolt compatible with the
IH 392 that was offered in the pickups, travelalls, and heavy trucks). I know a few Scout owners who are very pleased
with the 258 as well, and it's fairly easy to swap an AMC 360 into these.
I believe that Power Steering was an option, but it seems like all of them came with it. I'm not sure if power brakes
was optional, but they all seem to have that too.
First, as gmc999 said, take a look at http://www.off-road.com/~jweed/buildup2.htm
. This is Jim Weed's
guide to building a Scout for serious offroading. Second, contact the Binder Bunch (see the Binder Bunch
entry at http://www.off-road.com/~jweed/clubs.htm
). They're in Denver, and they are the best source of
knowledge on building Scouts for offroading, as well as being a great group of guys to go offroading with.
I used to be a member (until I had to move out of Colorado), so I'm definitely biased.
I've built my Scout along the lines you're describing. I started with a '75 Scout II with a 345 and a T18. I put
31's and Lock Rights in it, swapped in a wide T19, and bashed the body up a bit trying to keep up with the
rest of the Binder Bunch. Then last winter/spring I did a springover lift, 35s, cut and turned front axle, narrowed
dana 60 rear with 35 spline axle shafts, detroit lockers front and rear, rear disk brakes, dana 300 with 4:1 gears,
etc. Ran the Rubicon last September, and the Scout did great.
After saying all that, the preceeding assumes you're talking about a Scout II. The early Scouts ('61-'65 Scout 80,
'65-'71 Scout 800) are also an option. The axles weren't as strong (some had a dana 44 rear, but most of these
had two piece axle shafts. I believe that only the '71 Scout 800 B had one piece 30 spline axle shafts like the
Scout II). In general, you'd have to do more custom work to get 35s on an early Scout on axles strong enough
to handle the strain (though once you got them on, you'd have less overhang in the rear than with a Scout II).