For what its worth, I had/have similar experiences. New motor is rough during break in. Tried the old carb that was proven but it didn't like the new motor. I have no clue why since there was no air leaks. New carb is better but it is still tough to start cold. A lot of 4 stroking yesterday. Hotter plug today and although it was rough at first it seems to run better now. I did 15 miles earlier and let it cool for a couple of hours to test the cold start. It's not ideal but a lot better than yesterday.
If you have a Harbor Freight near by, they sell a compression checker for $9. I picked one up yesterday. I had never used one but it is quite simple. Pull the plug, screw the checker in the head, pedal and pop the clutch. The gauge will keep the highest reading.
FYI I think I read elsewhere that it is bad for the CDI to not have a load on it. So- you can leave a plug in the plug wire just dangling to the side while you check compression. Don't let the plug touch your thigh with shorts on!!
If nothing more, you'll have plenty of spare parts for the new kit.