Yes, the muffler or the spark arrestor can cause back pressure that will cause those symptoms. Is there a fuel filter inside the gas tank ?
Side note: I had a Kawasaki 500 3 cyl. 2 stroke that was bogging down after run for a while -- I FINALLY found that it was the exhaust baffles -- Cleaned them out and it ran fine.
Will the motor run strong for a short time (10 to 15 minutes) and then act as it has as the engine warms up if it is the spark arrestor? What's the purpose of the spark arrestor. Is it a machanical item versus an electrical item? Where is it located?
And, yes, there is a filter in the gas tank. But, I still drained the gas from the gas tank and cleaned the tank to be sure that I covered all bases regarding fuel delivery. I have not installed a new filter, yet. Roger