Hi Nodge, sorry to see you still have a running problem with the F2. Having spent 20yrs as a Honda trained m/c mechanic I fully agree with your points on lack of 'mechanics' about, just fitters these days (I try to repair everything if possible even if it takes me longer).
Anyway back to your running problems I can't see it being compression, or lack of, as in my experience compression doesn't really restore itself once warm e.g you can have valve clearances(on vehicles with adjustable shims/lock nut & screw) which are on the tight side, normally start ok when cold but once warm/hot will fail to idle properly & are harder to start. The fact that no2 cyl. was damaged & now runs ok & it's no3 that's causing you issues,( you've proved its not the injector itself) I agree with you it must be something electrical so I would continue along that path. All I can say is best of luck from someone who's only real experience is with petrol engines mostly without fuel injection ! So I will bow to your experience with all things with four wheels.