Firstly the Carol Shelby reason, "there ain't no substitute for cubes baby."

I know you're not dissing the R65 Tony as you do, as I do, some reasonable distance tours on them and I'm glad to have some verification that my one is not that far off others in it's standard form performance-wise (I've never ridden another R65 or known anyone else that has one) but sure am familiar with all the shortcomings you mention! The thing that keeps me interested is her ability through corners and characterful exhaust notes and maybe that it's only my second bike. My first was a gn250....
But back to the topic, I've been in touch with an airhead dabbler in NZ who has built many borrowed parts airheads and he recommended changing the final drive in preference to the high ratio 5th gear when I was reconditioning my gear box. I decided to keep it stock, but if I had a 32:10 final drive I'd definitely be fitting that. As you say, fitting that before fitting the heavier flywheel, then changing to the heavier flywheel would be a grand experiment.