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I am not aware of any major problems with the diffs or axles.
You know about the 5th gear issues with heavy towing, replacing the clutch with the genuine setup can be expensive.
The interior fan resistor can fail (just like any model vehicle) not a major issue, I have read a few reports about heater cores leaking (whole dash needs to be removed).
The electrics on the GU are pretty good not much goes wrong them apart from the alternator and occasional relay, (it is a good idea to run an extra earth from the negative of the battery to the chassis). Most problems are cause by the extra circuits people have added.
Common places for rust are the radiator support panel, around the front windscreen and on the wagons around the body rubbers (roof section) for the rear barn doors.
I'm not sure about the pump or injectors, but I would hope yours would be new (or at least were tested) when the new engine went in.
As MudRunner as said "do the NADS" and I also would replace the MAF sensor (for piece of mind).