So, this is where not being there makes diagnostics especially difficult.
I know you're describing the problem(s) the best you can, and you've been a good sport in trying different diagnostics, but right now, I haven't a clue what's wrong with it!
That said, here's a another idea: let's try to determine what's causing the "disruption" in the way it runs by looking at the effect on spark. Using either a spark tester or a clamp-on timing light (using a remote battery source), or both, see what the spark looks like when the engine runs poorly. If the spark is good and constant, then it suggests a problem with the TFI system; If the spark is getting "flippy" then it's something to do with ignition.