Sounds like you have a pretty good grasp of everything. If it is jetted properly, I wouldn't worry too much about rejetting to make it richer. Your plug color will tell you.
I do run my old bike one notch richer on the needle than perfect, but as glad2ride indicated, it is the full-throttle-to-sudden-no-throttle action that will usually get you. I am a bit paranoid, like you, but just use common sense (of which you have more of than many, from reading your post). Varying throttle on long stretches is a good safety measure--may not be necessary for most types or riding, but I do it too. I usually notice pinging while accelerating or climbing hill (detonation), loss of power (piston starting to seize), or a sudden increase in power (lean condition) right before a major problem. If you notice any of these things, address it quickly. But most important, service it properly and have fun.