My apologies for the delayed response..

I would begin with checking to ensure the timing and points are set properly.

Check the spark plug wires and make sure the are connected in the proper order and they are in good condition. If you are re-using the "old" spark plug wires they may be cracked in areas that may be causing some issues and they may be to "weak" for the new system.

This may sound odd, but turning the machine over in the dark would allow you to visually see any problems with the spark plug wires if they were cracked and "jumping spark". I have had cracked plug wires before and it drove me crazy trying to find the problem. I was able to find the problem this way - word of caution using this approach: if you see a spark coming from a plug wire, don't touch it until you turn the machine off. OUCH !!!

Also, I would double check any and all other wiring and their connections.

I am assuming you have tried all of these steps; sometimes it's good to check them again, although it does sound like a timing/points issue.

I have never changed out the ignition system on any of my machines, so my advice may be pretty general in nature; I've always re-built the mag and continued on continuing on. I know others that have made the swap, but I don't recall them having any issues.

Hope this helps...