UPDATE - With the octane boost the thumping is now gone!

It was raining on the way to work, so unless it's humidity related I'd say that the higher octane has temporarily solved the problem. I added about 1/3 bottle of
1606325131360.png
and brought the tank up to about 1/3 full to keep it concentrated.

So, is this a timing issue or a fuel issue I can tune out?

Timing- I was super careful during the rebuild to set it correctly (triple checked). Plus, other than this it pulls like a freight train- super impressive. I asked for drop in cams, so not as precise as dial-in, but should be close if not spot on.

Fuel- I just got the PC5. I plan to install it this weekend and load the tune my tuner did for me. It was converted to TuneECU, which is what's in there now. I also have Auto Tune coming in the next few days. My hope is that for what I paid for those used, I can fine tune it further for less cost and time than revisiting the tuner. I brought it in with a borrowed PC3 that gave him some trouble. Also, I remember him saying that the PC5 would allow fuel adjustments to individual gears, which could be good for solving this situation. Finally, someone here earlier suggested I get the POD-300 and I found it on sale new, so $hiite, why not. Now to learn how to use it all. Very glad it is not the Flux Capacitor or Torsional Bearing.

Thanks to everyone for their ideas and help. I think we have it diagnosed, at least.

 
UPDATE - With the octane boost the thumping is now gone!

It was raining on the way to work, so unless it's humidity related I'd say that the higher octane has temporarily solved the problem. I added about 1/3 bottle of
1606325131360.png
and brought the tank up to about 1/3 full to keep it concentrated.

So, is this a timing issue or a fuel issue I can tune out?

Timing- I was super careful during the rebuild to set it correctly (triple checked). Plus, other than this it pulls like a freight train- super impressive. I asked for drop in cams, so not as precise as dial-in, but should be close if not spot on.

Fuel- I just got the PC5. I plan to install it this weekend and load the tune my tuner did for me. It was converted to TuneECU, which is what's in there now. I also have Auto Tune coming in the next few days. My hope is that for what I paid for those used, I can fine tune it further for less cost and time than revisiting the tuner. I brought it in with a borrowed PC3 that gave him some trouble. Also, I remember him saying that the PC5 would allow fuel adjustments to individual gears, which could be good for solving this situation. Finally, someone here earlier suggested I get the POD-300 and I found it on sale new, so $hiite, why not. Now to learn how to use it all. Very glad it is not the Flux Capacitor or Torsional Bearing.

Thanks to everyone for their ideas and help. I think we have it diagnosed, at least.
I thought about the pod 300 but figure it would be better if I fix the bike first.
 
Update 12-13-20

Octane did help, but the bike started running worse and despite all that I have going on I had to set aside Saturday to try to figure it out.

Well, "stupid is as stupid does..."

IMG_3641 copy.jpg

All five caps looked like this. I changed them (the silicone hoses are still good), went ahead and cleaned and re-crimped all the coil wires, cleaned the crank position sensor, balanced the throttle bodies, and threw some Techron in the tank, but I know this was the culprit.

Went riding today and, once again, she's scary fast and runs like I remembered, starts faster, and purrs at idle like a kitten.

I still plan to install the PC5 and autotune in the next few days, but wanted to leave well enough alone for a while to make sure I was back to normal.

If it's been 36K miles (or a lot less!) since you changed your vacuum plugs I might suggest you do so now. It's a $3.00 fix for your E.D. (engine dysfunction).

Anyway, problem solved- thanks for everyone's help.
 
Update 12-13-20

Octane did help, but the bike started running worse and despite all that I have going on I had to set aside Saturday to try to figure it out.

Well, "stupid is as stupid does..."

IMG_3641 copy.jpg

All five caps looked like this. I changed them (the silicone hoses are still good), went ahead and cleaned and re-crimped all the coil wires, cleaned the crank position sensor, balanced the throttle bodies, and threw some Techron in the tank, but I know this was the culprit.

Went riding today and, once again, she's scary fast and runs like I remembered, starts faster, and purrs at idle like a kitten.

I still plan to install the PC5 and autotune in the next few days, but wanted to leave well enough alone for a while to make sure I was back to normal.

If it's been 36K miles (or a lot less!) since you changed your vacuum plugs I might suggest you do so now. It's a $3.00 fix for your E.D. (engine dysfunction).

Anyway, problem solved- thanks for everyone's help.
Totally unacceptable 25 pushups
 
One thread leads to another..... I think the knock is gone. The vacuum caps took care of most of it, but it was still presenting (less often and not quite as noticeable). Then the bike starting running really badly. With member's help on this post, What Now, it turned out to be the stepper motor.

So, it has me wondering.... when does the stepper motor do its thing? Does it by chance engage up to about 3K RPM? If so, could that failing SM have been tapping or turning on/off right where I was feeling that thump? I only noticed it in 4th or 5th gear, but then again I rarely cruised in 1st -3rd at 3K. Just curious if this all started with a SM going bad.
 
So the stepper motor has no smarts. It simply responds to commands from the ECU. In my case, there was pathological condition where whatever the stepper motor was/wasn't doing, was causing the ECU to command greater inputs, which would drive up the RPM. Then the ECU would recognize the RPM were higher than called for, and reduce. In my case, it would just cycle like that. Others here assisted me with that, and changing out the stepper motor, I have been fine since then.
 
So the stepper motor has no smarts. It simply responds to commands from the ECU. In my case, there was pathological condition where whatever the stepper motor was/wasn't doing, was causing the ECU to command greater inputs, which would drive up the RPM. Then the ECU would recognize the RPM were higher than called for, and reduce. In my case, it would just cycle like that. Others here assisted me with that, and changing out the stepper motor, I have been fine since then.
So, IF that were to happen at 2900 - 3k I'm just wondering if that caused the knock I was getting. I think I picked up on something @warp9.9 said about my giving more throttle in the video than was within range of the stepper. So, does the stepper stop doing its job at a certain RPM or throttle position? Just curious as it's all "academic" now. That part will be in the landfill come Monday.
 
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