when you set the timing, are you _just_ lining up the holes with the axis of the cylinder? thats a nice rule of thumb but youre basically eyeballing the whole process.
get an analog meter and you can test for continuity between the points and the ht coil (or something like that). you set it up so that as you rotate the cam, just as the points open you will see it on your meter. if you have a meter with a buzzer its even better... less to keep your eyes on and you can _really_ hear when they break. this allows you to determine the _exact_ moment at which your points break. much more accurate then lining the dots up or whatever.
also, you might want to consider dropping the engine, removing the head, and physically measuring TDC and mm BTDC. this is how i do it every time i set my timing, which is rarely because i do it meticulously. this, as opposed to the allen wrench in the spark plug hole method.
the only reason i mention these techniques is that every sloppy method you use to set the timing adds error to the final product... so its worth it to make sure every step along the way is as accurate as possible. some will argue whether or not the allen wrench technique, line up the dots technique, etc are "sloppy", and i do know they are widely used, but it just doesnt sit right with me. if you wanna eliminate variables, you gotta eliminate variables.
on an entirely seperate note, one thing you may want to consider is your wiring and grounds. i wish i could hear this knocking/pinging youre talking about to really say for sure, but i suffered from symptoms like this when i first got my moby. at high rpms, everything would vibrate so much that my spark would cut out and make a pop/knocking sound. imagine the sound made when you run over a dime-sized-diameter rock head on. i use that analogy because thats what i thought it was at first, when it happened about once a week.
i tried to fix this by swapping out novi coils. every time id swap out a novi coil, itd make it better for a while and then itd happen again. turns out it wasnt the changing of the novi coil that made a difference at all, it was the fact that every time i put on new coil, i made sure all the connections were good and the problem went away until they vibrated loose.
i eventually took care of the problem by simpling taking apart the wiring harness, making sure all the connections were squeaky clean, all the grounds were solid, etc. Double ground shit if you have to. sand down areas where rust or dirt or grime has accumulated. whatever you can do to make sure your wiring is tip top.
might not have anything to do with the problems your having at all, just throwin ideas out there.