Update -
Put 300 miles on the bike this past weekend, and scowled the whole way. The bike is just not right.... Nothing was going my way -- Even my new Zumo 595 (POS compared to my old 450) & Sena set-up was refusing to work right. Believe it or not, I also found a hole in the rear tire (100 miles on it) and had to plug it before I left for the weekend. It's just one thing after the next. Bike is starting to seem cursed...
Several observations:
1.) Shifting is still not right - had several false neutrals - and it even popped out of gear a couple times. (Related to Clutch Issues somehow?)
2.) Engine Vibration is definitely not within any normal range. I never used to have numb hands. The vibs actually move around between the left handlebar, right handlebar, and the pegs depending on fuel load (changing harmonics).
3.) Found a station with 93 octane and put in almost a full tank (6 gallons). Vibration seemed somewhat less - but might just have been the difference between full and empty fuel tank.
4.) Fuel consumption seems higher. I did average 48mpg running a full tank on secondary roads at 60-65mph (adjusted for speedo-healer's impact on odometer). But, on the freeway at 80mph, mileage seems to suffer more than it used to.
4.) If I rev the motor in the garage up to 5K, and then snap the throttle closed, there is a loud PFFFSSST sound. Almost like a blow-off valve from a turbo. Seems to come from right side cylinder head.
Therefore: I now suspect a vacuum leak??, which would explain the sound, vibration and "hammering" under load. (running too lean / detonation???).
In addition to all of this, the clutch basket rattle is much worse than the original motor, and the water pump is weeping. There is a definite "heart beat" in the bars coming from this area, so I'm thinking something is worn or damaged. Who knows what could have happened when the bike that the motor came from was wrecked....
Bottom line -- I think there is more than one issue going on...
I'm planning to start the process of stripping down the bike to hunt for a potential vacuum leak at the 5-way, and/or the Throttle Body insulators after work tonight. I'm going to go ahead and pull all the plastic again, and the fuel tank, front wheel, etc. From there, I'll drop the oil and pull the engine cover to re-build the water pump, bearings, and replace the clutch, springs, bearing, Judder Spring, etc.
On top of that, I'm planning to replace the plugs, plug wires, the thermostat, and various water and vacuum hoses, clamps etc. while I'm in there. My parts list is up to $600+ including the water pump parts, complete clutch kit, Wires and Caps, new TB insulators, etc., etc. etc. Haven't actually placed the order yet.... At this point, I'm assuming nothing was previously done, or done correctly - so I'm going to have check the valves for myself too. (Never done that for any bike, and I don't even own a set of feeler gauges -- so that will be a fun experience).
So much for my riding season. This is probably the end of it given work/kids/and Minnesota's very short summer/fall..... If I ever get it all back together and its still not right -- I'll be done with it.