This could be a tough one to diagnose because you've changed so much. You may have an issue with the CDI you have swapped. Pull out your spark plugs, and set them agains the head so they get a good ground and make sure you are getting spark to both cylinders. The next thing I would look at is to see if the engine was timed properly when put together, or if the valves were set properly. Is the engine cranking fast or is it struggling?
Jarrod Sheets
FD Racing
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