Speedo problem solved (I think), thanks to your advice, hamish.

I took a quick look under by the t-case, and sure enough the little black plug that goes into the sensor had a bad wire. I'm going to take a wild guess and say that once I get that spliced back together it will solve the speedo/odo issue.

As far as the noises go, here is what I can tell you. I'm certain they filled up both the tranny and transfer case, though I am not certain they used the right weight of fluid.

5th gear noise - I tried to replicate it in other gears but its clearly only in 5th, regardless of speed. It goes away when you put the tranny in neutral at speed and subsides when you let off the gas at speed. It is most noticeable when cruising in 5th and giving it a little gas. It's less noticeable at open throttle because of engine noise. It is constant and the tone of the noise does not seem to be tied to engine speed or cruising speed.  The best way I can describe it is a midrange-y hiss that sounds kind of like muffled static. It's not the kind of "oh " noise that would cause you to immediately pull over and stop driving, but it is definitely not normal and has appeared only recently with this new transmission.

The other noise I have had for some time now. It is clearly audible from the outside of the truck or with the windows down, and is especially noticeable when coasting at less than 30 mph through neighborhoods or cruising in traffic (the sound reflects off of other cars so it is easier to hear). It is always there regardless of the gear or clutch engagement. As long as I am moving faster than around 5 mph, it's there. It's tone is constant and does not rise or fall. The best way I can describe this is a very high pitched constant ringing or squealing.