firecaptp7
If the sidestand safety switch is still plugged into the main wiring harness, that would be my first guess as the source of the problem.
Some of these switches are installed so that the slightest movement of the sidestand will trigger them to shut off the engine power.
On a bumpy road, the moving sidestand could do exactly what you describe.
If you haven't disabled the switch, it is located under the sidestand. Follow the wires back to the frame seat upright and you will find where it plugs into the main wiring harness.
Unplug it and tape the dangling ends to something like the frame.
Of course there is a warning here. With the switch disabled, the bike can be started and run while the sidestand is still down.
Passing over a dropoff can cause the sidestand to knock the bike down so always check to see if it is up before you ride anywhere.
To answer the other obvious question, yes, you can run the motorcycle while it is resting on the sidestand if the transmission is in neutral. The oil pump will continue to pick up oil from the sump.
Another "cure" for the "misbehaving misfire" is to replace the OEM Bosch spark plug with a NGK #BPR6ES spark plug.
Be sure to get the kind with a screw off cap on top because the high voltage spark plug connector slips down directly on the threads under that cap.
If you try to use a spark plug with the large metal cap still on the top of it, the electrical connector will not plug onto it like it should. That will cause a lot of mis-firing.