Well guys we got it figured out!
It took some hours last night but we got the horsepower back. Some of this was me being a novice to the scope but the scope was able to confirm a lot of suspicions I was having.
After I got the scope dialed in and hooked up the current clamp correctly

I was able to prove that everything on the ignition system was working. I also was able to prove that the bike was advancing timing like it should. (For a little while I was thinking that maybe the TCI was not advancing timing which would definitely cause hp loss.)
I learned alot this time around on the scope. I learned how to set things up that I never have before and I was able to use previous bikes to prove good signals on this bike.
Enough chit chat, I am sure you guys are wondering what did all this!
Like I said, we checked compression and leak down, couldn't have been fuel because no matter how much fuel we added or took away it would not change and spark, after much debate, was also working like it should! If I had the compression waveform tool, this would have gone much faster. The customer had made, or he had someone make them for him...a set of "custom" baffles for the exhaust that are apparently extremely restrictive! After all things that make an engine run properly checked out, all I could think was that it was something outside of the engine so I started to look at the exhaust and waaay up there was these baffles. Removed them and did another run. The bike sounded so much healthier and you could definitely feel the seat of the pants power.
This was a challenge and really one to log away in my brain for later! I really appreciate all your guys input! I will post the hp/torque graph for you guys to see and also the known good ignition waves.