I finally got this done today! Nothing too bad, the worst of it was taking the seat and carpet out. Gave me a chance to clean under there though.Since I had them I replaced the nylon socket that the shifter ball sits in, and the gasket where the top bolts down to the transmission. Prior to my ownership, someone took that top cover off (probably when the clutch was replaced) and reinstalled it with liquid gasket instead of the paper seal that Nissan uses - so it's possible it was leaking there too.
The boot did have a nice hole in it and lots of cracks, so I feel sure it was leaking there. I didn't have any issues getting the new boot on by using some lube. The hard part was getting the shift knob off. The outer skin separated from the rubber core that screws on to the shaft, so I ended up cutting the cover and then using some big channel lock plyers to finally get it off. Guess I'll have to order a leather shift knob now 
I'll go tomorrow and get some fresh gear oil and change it and the differential oil. It wouldn't surprise me if I'm a little low on gear oil - it's getting a little hard to get into gear sometimes when it's cold outside and the truck isn't fully warmed up.
Heath