After doing some research here I figured out that my new motor was four stroking and not bogging like I thought. Plug gap was set at .025 so I opened it up to .032 and lo and behold more torque and just the slightest four stroking near the top end. I'll say its pretty peppy until about 2 miles or so and then I started to four stroke again, mainly on upgrades and then later in even in the flats around 17 mph just like before.
Well we arrived at the local sporting goods store about 4 miles from home to pick up some reloading supplies and when I got back on the bike nice and zippy again! About 2 miles later the symptoms repeating. Didn't have a chance to pull the plug when I got back but I did check the motor temp and around the exhaust port on the cylinder itself it was only 220 degrees and the rest of the cylinder was around 205-210 degrees.
It only has 57 miles on it so I will assume more break in time is needed