1982 Suzuki sp500 sputtering & misfiring

Hello, new to the forum and any looking for advice! I have been restoring a 82 Suzuki sp500 and have put my heart and soul into this bike and I am still having issue's. I have replaced the rubber intake manifold, exhaust gasket, piston rings, float, jets, head gasket, clutch, coil and spark plug wire, and many other items but do not relate to my issue I'm having. I will say that I have a aftermarket custom exhaust with sound baffles because the stock exhaust cannot be found. And a custom air filter on my carb (I have tried paper and foam) currently have a 3 inch pipe with a foam filter on. I am currently experiencing after firing and sputtering some of the time and other times my bike is running like a champ. The problem seems to happen the most when first started between 10-30 mins of riding and sporadically there after. Cleaned the tank and gas filter and carb several times with no luck. Carb has been adjusted to the lowest setting and everywhere in between but isn't seeming to make a difference. I have my finger on... jetting, new carb in general, or possibly a valve leak? Any thoughts or guidance is much appreciated! The bike has come to far forward to give up on restoring this classic but it was only made for 3 years and there is not much info for them so anything will help me get this issue resolved!