Rotting of the doors can be avoided by checking the drain holes at the bottom of the door, keeping them free of debris. Also wise to check for this before you buy.
Engines 3.9 v 4.0.
The 4.0 is actually the same displacement (bore and stroke) as the 3.9. Yes, the 4.0 is cross-bolted, but for an engine that does not put out much over 180 hp in that trim, cross-bolting really doesn't add much of an incentive. FWIW, both the 3.9 and 4.0 (and the 3.5, 4.2, and 4.6) are all variants of the Buick 215 built in the early 60's. The blocks produced by Rover have a different aluminum alloy (% of nickel, I think...) that make them stronger than the blocks produced in the '60's by Buick. Buick (or was it Olds...same block, same displacement) even turbocharged their 215 for over 180 hp from the factory, and hi-po guys have been pulling even more out of a "weaker" block than the 3.9. So, cross-bolting is moot unless you plan to stroke the engine and do some other fun modifications in the future.
Aside, from the cross-bolting, the 4.0 has larger mains which leaves more webbing between the respective journals on the crank (i.e. stronger crank)...again, a moot point unless you plan to pull more HP out of the anemic 4.0.
Finally, GEMS (Generic Engine Management System) vs. the distributer and 14CUX (CUX as in "sucks"). I prefer OBD-1 engine management (I also prefer the distributor), only because in some states, blowing an OBD-II code, whether your vehicle meets smog or not, can cause you to fail emissions/inspection. The GEMS is nice as it does incorporate a knock sensor to retard the timing to reduce the occurance of detonation...probably more of a benefit if you plan of continually overheating your engine...but since both the 3.9 and 4.0 are relatively low state-of-tune engines, detonation is not really a problem, and the 4.0 does not use it to add any power.
The 4.0 does have slightly different cam timing events (same intake/exhaust durations between the 3.9 and 4.0, but the lobe centers are different) which contributes to the added 10+ hp between the 2 engines.
Other stuff to look for: sunroofs (have been known to be problematic and expensive), check for rust around the alpine windows, check for rust at rear passenger doors around the top of the fender (where the pillar meets the fender).