you said you rebuilt your carb??? sounds like you have a choke issue. i wouldn't jump to conclusions of your exhaust system being the problem but i wouldn't say its the carb right yet, look at filters first. i drive a 20r and rebuilt the carb too. at first it was perfect hot, cold. start-ups and everything had a great cold to hot kick down. put it this way it was harmonious. now i came back from deployment and mechanically it was a little dry and the choke works but doesn't open enough on start-ups so its spits and sputters with excessive fuel not burning from lack of air. ya ya choke works by restricting air but this is too much restriction. after it gets warm im fine but in your situation i am leaning towards your rebuilt carb being the problem. when it spits look to see if the butterfly is open and you might have a jet getting clogged too. if it spits smell your exhaust for fuel, if so check the butterfly. might have a bad diaphram in the choke assy. i run a stock manifold into a 2" pipe to 2" glass pack out to 2" tail pipe. i have no issues but as marlin mentioned if you open the exhaust too much your back pressure (which helps close the valves effectively/timely) will be lost and there for reducing your performance, no engine braking, it will be too free so to speak. it may increase your highway performance but on the trail it will be a dog. i wouldn't go above 2" on the exhaust, if you do, have a 1 3/4" muffler to slow the gasses a bit.
