I took the u joints out and got replacements (same type) just in case that was the culprit. That didn't change anything, so I flipped the rear of the driveshaft 180 degrees at the pinion yoke and unfortunately I'm still getting the vibrations. I didn't spend a lot of time messing around putting some tire weights on the shaft, but I did try a couple spots near the rear and didn't really notice any change one way or another. I figure if I'm going to go down this road I'll need a lot more free time to test things. Here is some additional information below.
I strapped my gopro underneath and took videos of the front and back u joints in motion. I uploaded these videos to my box storage account and have hyperlinked them to this post. I can't make much out of these videos, but maybe someone else can.
In the first video of the front u joint (https://uofi.box.com/s/5dlvlklwx8bs4yf2n4dccyharyvap0bd), up until around the 2min 15sec mark is just me backing out of my drive and driving to the main street before I accelerate up to around 70mph. The vibrations really start inside the cab around 65mph and increase dramatically from there. You can notice the shifts around 2min 19 sec, 2min 23sec and 2min 35sec. I think I started coasting around the 2min 50sec mark or so.
In the second video of the rear u joint (https://uofi.box.com/s/ufpxa9i9d66my752qeacpfmeidtwhih2), up until 20sec is me getting turned around. I can't quite make out the shift points as well in this video, but I think a couple are around 33sec and 45sec. I think I started coasting around 52 seconds, the rest is just me driving back to my house once in the neighborhood.
The only other thing I can think of to try before I start adding weights and moving things around is to flip the slip yoke 180 degrees on the front of the driveshaft. Other than that, I'm at a loss and may have to just take it somewhere.