Don't know where you want to go but I can tell you what I would do next for what it's worth. It seems like it could be a timing issue and since the flywheel key is good, valve timing or a bad SAM would be what I would check next. Since you probably don't have a SAM tester I'd start with the possibility of valve timing being off. This is why I asked if there were any signs of the engine ever being over heated. If you over heat a Command Twin, it can cause the gear on the crankshaft to expand and that can let the crankshaft turn inside that gear causing the valves to be out of time with the pistons. To check for signs of over heating I'd remove one or both of the rocker covers and look at the area of the head between the valve springs. If the engine has been run clean and cool any discoloration cause by oil should be fairly light brown to a golden color. If the engine has been over heated that area will probably be very dark brown and thicker than just a film. The rocker arms could also be dark in color. If you do decide to remove the rocker covers and find it very dark inside the next thing would be to check valve overlap to see if the valves are out of time. There is no other way to check valve timing on a Command Twin. If you get to that point and find you want to check valve overlap let me know and I can walk you through how to do that if you don't know.