Hi Dave,
I got my bike in pieces, so much of the way I assembled it was through trial-and-error. The rear engine plates on mine have washers about 1/8" thick welded on the right (timing) side, and the gap between the plates away from these welded washers is 3-5/8. The frame mount is 3-1/2", the same as the top mount on the transmission. On mine, I had a 1/8" spacer for the transmission which I fit between the mount and the plate on the right side (As I recall, no spacer was needed for the bottom tranny mount). There's a sort of J-shaped bracket that holds the front of the rear fender. I found it works best if held in place by one of the studs going through the frame into the rear plates. One of my studs was 1/8" longer than the other, I assume specifically for this purpose.
On the front mount, there is a middle spacer on both the top and bottom stud.
The center stand also has spacers - one in the center, through the coils of the spring, and one on the right, about 1/8". One end of the spring hooks around the cross-brace of the stand, and the other hooks into a hole in the right engine plate. There's a retention clip for the stand that screws to the base of the frame vertical section with two small screws, I think 2BA
For the long, square stud that runs through the frame, engine plates and footrests, there are 3 spacers. The center one is about 3-5/8, the left (primary) side is about 1/4" and the right side is about 3/8".
You need the footrests in place before you can mount the primary, and to install the outer primary, you have to drop the brake pedal as low as it will go, and slide the stator over the rotor with the primary cover almost vertical, then rotate down to horizontal as you slide it in around the footrest perch.
