The LSDs are clutch-based, but Nissan tapered the numbers as the model years progressed. These are the numbers I compiled from Factory Service Manuals when I was rebuilding them:
At least for the rear diff (model H233B), there are no other LSD options, only three lockers. I rebuilt some using new OE parts a few years ago, but I was told I depleted the supply on some of the thicker discs and plates. However, buying a junkyard LSD from any of the above trucks will yield extra pieces to rebuild; although the parts will show some wear, it's the thickness of the pieces that'll matter here. I've been able to build them up to about 160-180 ft-lbs and that has performed well for off-roading, combined with a front mechanical locker. I've still got a spare LSD at 165 ft-lbs; rebuilt it from the parts I had, but never re-installed it because it was replaced by a locker.
That's how I'd go with the 5MT: start there, and hold out until you find it. Personally, I've always been a stick guy; this truck is my first AT. I've appreciated it to some degree, but I wouldn't mind an MT again.
So, hopefully this won't detract you from looking to buy an R50, but I've always termed the truck as being Nissan's redheaded stepchild, or otherwise bastard truck. I've named it so because it's very different from anything that it should be similar to. Much of the drivetrain is very similar to 89-04 Hardbody, WD21 Pathfinder, Frontier, and Xterra models, but not the same. The front diff (model R200A), for example, is unlike every R200A that ever existed on those trucks—ours is high-pinion/reverse cut, everything else low-pinion/standard cut. As such, we only have OE gearing options (4.363 or 4.636). The rear axle, fortunately, is basically the same as those trucks, and there's a lot of interchangeability (I run disc brakes from a WD21, for example). Transmission is actually of heavier duty than the others, except late Xterra, I believe. Same transfer cases (excluding the all-mode version, which wasn't used elsewhere). Suspension is totally different. VQ never appeared in any other truck until the stroked VQ40 showed up in MY05 Frontier, Xterra, and Pathfinder...and even that is a very different engine.
There are some parts overlaps among VQ35's, but Nissan made a lot of subtle changes on them. Kings of the spare parts indeed! Starter placement, oil filter location, even all the intake plenums were basically unique by model. You don't have the overlap that existed for older Nissan car models. But at the same time, I'll acknowledge that I've seen very little in the way of engine performance mods on the R50 done by owners...it would likely be a heavy investment of time and money to research, as no one specifically lists the R50 as an application for performance parts. No headers, no cams, no turbo kits, nada. Fortunately, the data is there via the FSMs as a starting point to at least see if, dimensionally, parts might work. I use RockAuto for a LOT of parts cross-references, and of course Google image searches (I find that eBay listings for engines also have lots of pics). Parts.nissanusa.com and nissanpartsdeal.com also help greatly for parts cross-refs.
That all said...the R50 is a great truck if you can get over how different it is from other Nissans, and can deal with basically no aftermarket support. The bastard qualities, in my opinion, are what make it perhaps the best truck Nissan has produced, including 05-18 trucks. Outside of the PV issues, the VQ35 had far more power and torque than any VG that was offered (including the supercharged one found in Frontiers and Xterras), and far less problems than the VQ40. High-pinion front diffs are better for off-road. Heavy duty transmission, standard. 5-link rear suspension. While I hate having McPherson struts up front, let's face it: the truck handles like a car and you'll come to appreciate that. The drivetrain is far more stouter than anything 05-18, including Titans (but maybe excluding the new Titan XD). The unibody has offered no less rigidity or flexibility than a framed truck. Better looking interior.
Sorry for the long post, and perhaps my final recommendation: I'd look for 01-02 models. Outside the IACV/ECU issues and PV issues, which can be addressed by preventative maintenance, the other notable is that they were drive-by-cable; 03-04 was drive-by-wire...more sensors, more limp mode, more expensive throttle body. I also think you'll have more hope finding your 5MT in the earlier range.