Given a free hand?
NOT used the Peugeot gearbox - I'd prefer a Muncie top-loader, even if it IS a four-speed.
Door hinges should be bolted at both ends, not bolted at one and welded at the other. (Yes, you can bolt door hinges to a unibody.)
Either set up a higher intake manifold (for less angle through the cylinder head) or design a cross-draft head. Either one will help to make additional power.
Two words - roller valvetrain. (for longevity's sake.)
Install an "overdrive/underdrive" or a "gear splitter" between the transmission and transfer case, to allow for heavy towing or long-range freeway cruising (or, better selection of axle gearing.)
Two words - heavier axles. Dana 44/60?
Three words - more common parts. AMC was jokingly meant as "All Makes Compatible" - using some more Chevvy parts would make field service easier, and would make parts easier to find (Chevvy parts are easier - and usually cheaper - than ChryCo parts, and don't get me started on RENIX...)
Fewer vacuum lines, and make a "core harness" out of copper or steel. Get rid of those hard Nylon lines - I never did like those...
Elimination of the C101/bulkhead pass-through plugs for something a little more solid and sealed - even plastic Amphenols would be an improvement.
Provision for power to upper-deck lighting (exterior.) Again, Amphenols are a nice choice for this.
What else? I'd have to think on this for a few days...
5-90