To make following this post easier: Can you re-list: Current Symptoms / Troubleshooting performed thus far / Mileage when performed / current mileage?
I will list all symptoms, some of which are not concerning and the major symptoms. The minor symptom is at cold starts, the bike revs normally but 30 seconds later the idle drops while the bike is still cold and it warms up on what appears to be normal running but rough idle, it smoothens out once warm. If this issue isn't related to what is listed below, then fixing this wouldn't be a concern to me.
The major concerning symptoms is what I call the cut-off on High Revs/Heavy Loads. This occurs about 75% of the time and at other times it runs normally. When accelerating aggressively to higher rev's the bike hesitates to go above 11,000 revolutions. The hesitations works in a matter where it appears the engine cuts-off for a short moment less or equal to 1second or typically acts as a rev limiter but it bounces past 11,000RPM but it is a mess anything above 11,000RPM, if I can get it past. The bike currently has 80,600 miles on the odometer.
This issue became much more relevant after the clutch was changed out. However, the issue existed before the clutch work but was very rare and minor. This recently made me believe that it could be a bad pick-up coil since it's attached the the clutch cover.
I recently replaced the fuel pump with a used one purchased from eBay (80,200 miles). This didn't appear to fix anything. I then followed with replacing the ECM with one from another bike (1-year newer model <2008>, same day as the fuel pump). Issue seemed less relevant but it did it, so this goes back to the 75% of the time this occurring. So that ruled out on being a bad ECM.
After doing further research online, I see people claiming that it could be a bad fuel line, bad/loose pick-up coil
, or a cam chain issue. A mechanic locally had informed me that it could be the Main Harness or ignition coils. With my cam chain I have the manual adjusting cam chain tensioner if this helps in anyway of troubleshooting this issue. I've had the manual cam chain tensioner for over 40,000 miles now. I began noticing this issue as it became more relevant, I would say this issue was noticed for about 2,000 miles now, clutch was changed 4,000 miles ago. However, I didn't ride the bike hard for the first 2,000 miles, no particular reason, so it's hard to know if this issue happened immediately after the clutch or at a later time.
I hope this is detailed enough and hopefully I can get some more suggestions. Any helps as I'm completely lost as to where to diagnose.