Here is how I did the alignment on my Honda 350 racebike. I had put a CB motor in an SL frame so there were some minor issues with wheel and sprocket alignment.
First we measured from center point of swingarm pivot to the center point of rear axle to align the rear wheel. Then we aligned the front wheel with that and spaced sprockets to work with this setup. It worked and the bike handled just fine.
Ken Essex, we may have crossed paths back in the late 80s as I was racing WERA Vintage 4 & 5 in '88-90 in the Southeast.