Hi Blaine, nice looking project. Not uncommon to need a little spacer there, its possible there is a slight deviation in the frame rail, or the bottom of your trns mount has worn away a little over the years. As long as the kicker gears mesh fine, and the motor mount is solid, you should have no problem. You will want to adjust the brake linkages rods a touch too, to prevent the linkage from snagging on the case. The clearance is minimal to start with, and most primaries show evidence of a little rubbing there at some point in their life.
Once set right, I usually use a longer bolt and double nut it, using nylock nuts, but whatever you use, make sure that rear mount stays tight, and check it regularly before riding, along with the oil level.
