Welcome! It's a good truck to look for, and you're asking the right questions. I'll take a stab at them.
Check the strut towers for rust, as Astrorami mentioned. This was a recall item on older VG33 models, but not 100% sure it was an issue for VQ trucks. Doesn't hurt to check. The tower area will include where the top of the strut mounts, and the entire wheel well area basically. I'll add that other points I've seen are by the rear subframe mounts (where the tail of the lower control arm bushing is) and also the tail of the fenders, especially is the truck has any fairing or mud flaps there. Mine's a desert truck, but I've cleaned out tons of sand and dirt from the area.
The IACV and ECU issues I think were only on 2000-2002 trucks, but don't quote me. Can't attest to any repair questions, though.
Orange sticker is usually the best way to tell for LSD. If you've got a VIN, plug it in at nissanpartsdeal.com and check the Power Train > Rear Final Drive parts section. Results are filtered by VIN, so it references the LSD parts diagram, I'd presume it to have one. However, the LSDs were pretty weak. I've rebuilt a few to have much better numbers.
I'd plan on inspecting the power valve screws for any year unless you know it's been addressed previously. I'd check the VIN plate on the motor to see if the motor has been replaced, the likely "fix" from a previous failure. I know of two 2002 trucks that have succumbed to it.
Can't say I've seen a 5MT swap. The MTs were pretty rare, so that's probably a limiting factor, but they show up every now and then (another new member was just asking about this). I'd say it requires any typical amount of AT-MT swap effort. If starting from the All-Mode truck, yes, you'd likely have some complications because of input signals between the control modules. You'd have to bring over the MT's Part-Time system. That may open a different can of worms. I would assume a Z33 transmission would not work. One notable about the R50, in general, is that it deviates largely from other Nissans that you'd expect it to be more similar to. The VQ35 is one of those things...it's just different enough than the 350Z, FX35, and other RWD/AWD options.