Sorry, I've been out of town for a few days.
Good video! I've seen it before, but it was a long time ago (years). It's a good reminder. I made sure when I welded in my rear spring perches to get the pinion and t/c flange parallel when at ride height. I also verified tonight it was in phase. I think the problem is the angle the picture was taken. However, I did remove the yoke and u-joint to clearance them a slight bit about 2 weeks ago before realizing I couldn't clearance enough to make a difference. Since then, I've had a slight vibration above 50 mph that I didn't have before. I just assumed it was from the amount I clearanced throwing off the driveshaft balance. It just struck me tonight after reading your post that I might have put the yoke on 180* off from where it was balanced. I'll have to check that. Sometimes I amaze myself at my stupidity. I marked the driveshaft before I took it apart. Then I painted it while it was apart. It's hard to see marks when you paint over them.

I put it back together and didn't really think about it again until tonight.
Yes, right now I just have the stock FJ40 u-joints/yokes. I have heard that the mini truck driveshaft yokes offer a better range in operating angles. Anyone know for sure before I lay out some money?
I took Mr Jits' advice and threw a relay into the brake circuit. It was way easier than fabbing a bracket to mount the one I had to the brake pedal. Honestly, I can't tell much of a difference in how it drives and shifts. It may release the torque converter a bit faster when hitting the brakes, but otherwise I can't tell much difference. Regardless, I'm glad the system see's the correct electrical input now.
I also pulled a leaf from the front spring packs yesterday. The good news is that it sits almost perfectly level now. Not the best pic, but you get the idea. And everyone loves pics.
The bad news is that my 2" drop pitman arm slightly rubs the front spring pack before I hit the bump stop. The 2" drop was perfect with a 4" lift. But with an SOA and high steer arms, it is too much. The relay rod actually sits slightly lower than the tie rod now. I'm going to try a flat pitman arm. I took some measurements because I was worried I wouldn't have enough clearance the way my Scout box is mounted. It looks like I'll still have about 1/2" between the castle nut and frame with a flat pitman arm. As usual, one thing leads to another.
I still need to make the skid plate and re-do the anti-wrap bar. I also have to swap the military wrap on the rear springs. Finally, a little bit of body work to avoid having the rear tires do it for me, and I'll be able to wheel this again. I'm tempted to add an inch to the wheelbase because I have the holes in the spring perches to move the axle back 1". Since I have to do body work anyway (I was hoping I wouldn't have to when I set everything up), an inch might help my driveshaft angles a bit. I'm also going to have to order some front shocks and re-do all my bump stops. Anyone have a favorite bump stop they want to recommend? Considering how long my list of things to complete was 3 months ago, I'm happy with this small list.
I've been driving it around town, but it's killing me not being able to take it off road. My original goal was to have it wheelable by July 1st. Obviously that didn't happen. My next goal is to have it done for Cruisin' The Woods at the end of September.