Poppin, don't feel bad about the confusion, but it will go away when you really get into your iinstallation. Some key points to start with. 1. Clearly mark your frame where the axle centerline is going to be. Hopefully, you have a rubber axle bumper bolted on and you can use the hole as a reference point. 2. Set your frame level from side to side and front to back. 3. Determine your ride height for your empty truck and determine how far it is from the bottom of the frame and the top of the axle housing. WRITE IT DOWN because you will go back to this many times. Now you are ready to start following the instructions. Your parallel bars will mount on the axle pad in the front and they must be level when the axle is in place at ride height and is set so the face of the tranny shaft and pinion input shaft are parallel with each other (same degrees from vertical) Axle must be centered under the frame rails (side to side). When this is all in place, I spot weld the axle housing to the jack stands so it does not rotate from this position and stays put. I then decide how far inboard from the backing plate I want to mount my parallel bars, which usually is directly under the center of the frame rail. I will place the axle pads on the axle and use a scribe to mark their locationswhen I've measured this about 4 times on both sides, I will place the pad on and use a level on the back side where the shock mounts to get it vertical and tac weld it in place by puting a tac on each side of the mount, check my scribe lines, recheck the vertical position and add another tac to each side and move to the other side of axle and repeat. Now you can attach the bars to the axle mount and start locating the front mount on the frame. Here it gets harder because you want the bars to be level with your ride height, level with each other and PARALLEL with each other. When you have them clamped in polace and you can no longer improve any of your measurements, then tack the front mounts in place similiar to the drill described for the axle mounts. I'm sure your instructions say all of this in so many (probably fewer) word. Now you affix your shocks to the axle pads. You want your shocks to be vertical and tangent to the axle. Ideallly, the shock should be perfectly vertical as seen from the side and from the rear(front) but can be tilted inboard slightly if you have the correct mounting configuration.
Lets go back now and revisit your instructions about setting pinion angle by adjusting the length of the parallel bars. If you do this, then the pads rotate with the axle and you are no longer vertical with your shocks and that becomes a problem. Yes, you can make some slight adjustments to correct slight errors adn you may end up spliting the differences.
Is this a triangulated 4 bar kit or does it use a panhard bar? If it's triangulated,, let me know and I will be glad to address the other two bars.