There's a lot more to this than meets the eye.
If you measure the distance between the rods on the front and rear of the front tire it will tell you is the wheel is straight.Then you proceed with the rear wheel alignment. Don't forget here that the distance being about 8' from the rear wheel to the front measurement will give you such a small degree of error in the adjustment at the rear wheel that I doubt it could be done as accurately by other means.
The movement of one thread (rotation) on either rear wheel adjuster in either direction will move the front of the rod at the front wheel in this jig about 3/8" so you can see just how sensitive it is due to the extended length of the rods.
There should be equal distance when measuring at the front and the rear of the front wheel when setting up at the front wheel.
It's also a fact that if you rotate the alignment rods on the setup, you will see that they are not exactly true either. I rotate them until I find any discrepency is facing downward on both meaning that any slight discrepency is now neutral. There will always be some deviation in a rod this long for starters.
It sounds like a bit to comprehend but it works well and the setup is much easier than it sounds here.
As far as the foot pegs, I really don't think that all things are equal there when they are built. The baggers being adjustable enter a new problem here also.