I think you have proven that the ignition is the problem. It is interesting that you could get the engine to run at all with the wires and the rotor inverted. One of the things on these little engines that is maddening is when you have compression, spark and fuel. That is the triangle correct! it will run. Not so my friend, spark out in the open is not the same in compression. There have been a few of the coil boxes bad straight away, I think as you move the timing with the flipping of the rotor, you are putting the spark in a place that is not under as much compression and that is how it is then at least starting.
One thing that has happened to me also is that the engine floods out easily, (usually after standing for a while) and then with a crankcase full of fuel it tries your patience. I have put the throttle wide open and given it quit a bit of puff to get it to fire, it blows fuel all over the rear wheel and takes a block to clear. Keep us posted, but it sounds like the coil. Have fun, Dave