If you made all of the modifications at the same time it will be hard to pin point where the problem might be. This is why we always suggest doing one thing at a time. That way if something goes wrong you'll know where to start looking.
My first thought is to start over with all stock components and make the changes, one at a time.
If the engine runs stock you're way ahead of the game.
Otherwise start with the basics: Fuel, Air and Ignition. Some will say compression too. I can't argue with that.
I'd start with using the factory CDI. They perform just fine and they're simple and usually trouble free.
As long as the head and head gasket aren't leaking they probably aren't the culprit.
The pipe will require some carburetor tuning to get the most from it but it shouldn't keep the engine from running.
Good luck. Let us know how you're doing and/or what you find.
Tom