Bonanza Front Fork Boot & Rear Shock Questions

Im just putting together a BC-1200 that I bought a few months ago after re-paint and general restoration.
I'm noticing that the bottom part of the chrome upper for the right rear shock has been beat in pretty good, in order to clear the chain on a larger diameter sprocket. Did Bonanza build them this way?? Seems that a better idea would have been to put a spacer behind the lower shock mount to clearance the shock outward some.

I have put on new rubber front fork boots. The hole in both the top and the bottom of the boots is the same size, and fits the lower fork leg perfectly, but not the bottom of the upper fork where it is larger (the blue painted part where it meets the lower fork leg. Are the boots meant to ride on the lower fork leg only, or is it supposed to be stretched out to go over the bottom of the upper fork leg?