Just an off chance but check the front upper motor link that's bolted from the front head area to the frame on left side... The bolt at the frame may feel tight because of factory locktite but really check to make sure its bottomed.

 

As you have a slew of suggestions, and some really good ones at that. Believe it would serve you better at this point taking your scoot to your favorite shop and have them analyze/troubleshoot it IMHO.

As internet blog troubleshooting can get real hectic at times, wish you luck!

B Bop

2012 FLHR (Road King) Ember Red Sunglo & Merlo (stage II)
Cruise Control, ABS, Chrome Aluminum Profile Laced Spoke Tubeless Wheels, Security Package, Saddle Bag LED Lid Spoilers, and an array of accessories that enhances nostalgic appearance & blood curdling performance.

Generally, in life you always miss 100% of the shots you do not take.

 

Have you smoke tested the exhaust?

 

I had a loud tick that i noticed after i changed pipes/muffler and air cleaner when i did stage 1. I kept thinking it was an exhaust leak. I tightened the bolts a couple times and still had tick. Motor ran fine, so i just assumed it was a leak.

i took bike to dealer for other service and they noticed the tick and pulled things apart and found 1 of the cams had the coatiing come off and it damaged cam, lifter and oil pump. They changed it under warranty and all better now.

My dealer ordered a replacement cam and it arrived from Harley pitted and defective. Harley overnighted another...that one came in pitted. My dealer wasnt getting help quick enough, so the owner found a good one at another dealer and bought it. I wonder how common this issue is.

2016 Limited 10k miiles

 

From what is described and the miles this answer is likely the winner.

 

Found it and fixed. Decided to take off the exhaust and replace the gaskets. Removed the heatshields and noticed the muffler backed out of the headpipe. It was all the way past the slots creating atleast a 1/2 inch gap. Pushed it back on and fired it up and bingo tick is going. The crazy thing is the tick I could of sworn was coming from the front cylinder and no where near the rear of the bike where the leak was.

 

Just saw this thread. My 2012 SG was making a noise very similar and I found one of my Rinehart slip ons was loose. I over tightened the clamp and and ended up having to buy a new clamp. Bingo! noise gone.

 

Nice work! Now you can ride in peace knowing your engine is fine.