RE: set up problem?
Welll, Chocorrol. It all depends on your experience with working with four stroke engines. By design, they are somewhat more complicated than a two stroke... and of course, it also depends on how far you want to take it down.
What you are experiencing sounds more to me like a tuning problem than anything else. I would focus on getting that part of the process corrected and perfected for that engine and not worry to much about cleaning the engine out as you suggest.
CGr.