Spyk,
What year is your bike? Is it new, or is it a few years old. Has it ever run well for you? Did it run right before the dealer made changes?
My Speedmaster is about 4 years old. I was losing power, and I saw my plugs were black and fouled. I replaced the plugs and plug wires and got back some performance. It cleaned up the fouling too. Later I replaced the coils and got back all the power I had lost. If your bike is older, this is something to consider. If it's new, then, well, nevermind.
If I were you, I would install new plugs. You need to do this periodically anyway. Do it yourself. If you don't have a good plug wrench and a plug gapping tool, go buy them. I would also buy a torque wrench. After I started using a torque wrench, I found I probably had been over tightening my plugs. Anyway, new plugs will give you a reading on how well you are running. Don't count on old plugs to give you a good reading.
Have you fiddled with your air/mix screws? They might need to be adjusted, especially after changing to 45 pilots. I doubt if the dealer set them correctly. That might make a difference at low throttle. Excluding all other changes, the bigger your pilots, the less turns out are needed on the air screws. I think Greybeard has a good writeup on setting the airscrews. Search for it.
You might also get a little boost by pulling the snorkle from the airbox. It's an easy mod, and it's easy to put back if you don't like it.
Finally, don't worry about a little popping on deceleration. Unless it's extreme, it's normal on a well tuned engine.
Good luck,
Cody
