@vtrn_raptor You have just answered your own question there dude. Just like fire, combustion engine's require three elements to produce combustion or energy; Air + Fuel + Spark = Energy. If the mix is wrong then the combustion will be imbalanced. As long as your spark plug is fine you should be producing a good spark to ignite the fuel and air mixture. Did you fit a new spark plug after the rebuild? If not then I would recommend that you get a new one ASAP.
Too much fuel will cause the engine to run rich, with un-burnt fuel getting pumped out of the combustion chamber by the piston. Basically the mixture will be too wet. Too much air will cause the mixture to run lean aka dry. In effect too much air will dry out the mixture. Have you looked at the spark plug since the rebuild? Refer to a Haynes manual to check the colour of your spark plug? This will tell you if the mixture is correct or not? Adjust accordingly if required? If the mixture is fine then I would look at the timing next, perhaps the engine is miss-timed, which would give you a rough idle and poor running at RPM.
If your bike runs good with the choke ON, that's because you are adding fuel to the mixture, aka over-fueling, which tells us that your mixture is wrong. Perhaps it was poorly set-up by the previous owner, or there was an air leak due to the top-end or a gasket being worn. Now that you have an air tight barrel, your engine requires a different set-up, one which is as it should be.
If you don't have a Haynes manual for your bike then I would suggest that you get one ASAP. They are a wealth of info for home maintenance and have a great section's on diagnosing problems too. There well worth their weight in gold, plus there's always some for sale on ebay. 😉