The factory air intake system is actually a pretty good CAI system in its own right, so there's really no need to spend money on an aftermarket system. Drop -in cloth filters like K&N offer better flow (not that you'll need it) but also pass a lot more dirt through it compared to paper filters. Most of the performance will be mental than actual, if you know what I mean.
Short tube vs long tube depends on a number of things, but at least (if you purchase a quality brand) they don't crack like the factory manifolds. As far as the long tube, they are illegal unless you only drive off-road. Of course, there are people driving them on the street. Depending on how strict your state vehicle inspection is, the could fail it for emissions "tampering." The long tube converters offer better flow, but eliminate the upstream catalytic converter. This causes two problems. You will need to install a CEL eliminator (O2 spacer) on the rear oxygen sensors to trick the ECM and keep it from triggering P0420/430 catalyst efficiency codes and illuminating the check engine light. The long tubes also cause the engine to run lean unless you get a custom ECM tune; UpRev is your best option.
With short tubes, you may be able to find a set that passes your states emissions if they are strict about that sort of stuff. They correct the manifold crack issue and offer better flow and direct-fit in place of your manifolds.
Most of the aftermarket, post converter options will make your Pathfinder loud or "drone", but at least the V8 sounds a lot better than the V6. I'm not sure if Gibson has an option for the V8, but they are one of the better sounding exhausts on the Nissan trucks.
Best mod for your truck, if it still has the factory radiator, is to replace the radiator with an aftermarket unit to prevent the possiblity of the trans cooler failing and ruining your transmission.