Just because you can blow through the muffler doesnt mean it's not restricting. Try unbolting it and see if it runs better.
Now would be a good time for a multitude of tuneup stuff too.
New gapped spark plug, new air filter, clean the carb until it shines (Make sure you screw the two adjuster screws all the way in and write down how many turns it took so you can put them back EXACTLY where they were if you want it to idle right ever again.) If you change your trans oil, use straight SAE-30 engine oil, non synthetic. People have noted performance losses from anything else.
Also check that your auto choke isnt staying on. Once the bike is totally warmed up, unplug the auto choke box line that runs to the carb and cap the nipple and the hose as well as you can. If it runs at speed better like this, the choke box is probably getting sticky.