@J Cagg

It was a busy and hectic couple of months, but I would like to provide an update to this thread.
Continuing from where I left off in this story/repair....
I tried my best to clean up the groove in the pinion shaft with some emery paper.
Installed the following parts:
Andrews 48H cams
S&S cam plate and S&S oil pump
S&S premium high performance tappets (330-0175)
Fuel Moto adjustable pushrods (930-0145)
Rocker Lockers For Harley-Davidson Twin Cam Motors from DK Custom Products ( DK-RL-TC)
Replaced both front and rear rocker housing breather baffle assembly (HD 26500002)

During reassembly, one of the first issues I ran into was with the Rocker Lockers. I read the instructions before starting out and removed the rocker arm supports from the motorcycle. I then used the "Teflon Centering Tool", to center the rocker arm shaft. The first brass bushing installed without any issues. The second brass bushing "mushroomed", due to the rocker arm shaft not positioning properly. What's strange is that I used the "Teflon Centering Tool", to make sure the shaft was correctly positioned. Obviously, it wasn't and I should have carefully checked that the shaft was correctly positioned inside the bolt hole. I'm not sure why the rocker arm shaft didn't correctly position itself after I knocked the "Teflon Centering Tool" through the bolt hole.
Maybe due to the mileage on the motorcycle, the shaft didn't rotate and the "Teflon Centering Tool" slightly deformed when passed through the bolt hole. The other two brass bushings installed without an issue. I contacted @DK Custom Products and they quickly sent me out a new brass bushing! First class customer service! I made sure that the rocker arm shaft was positioned properly, and the new brass bushing installed without any further issues.

I adjusted the pushrods and buttoned everything up. I installed the Dynojet Power Vision map I received from Fuel Moto and started the motorcycle up.
The motorcycle started right up, but ran like ****. The bike would stumble, stall, run rough, and had no power. It was basically unusable. My first thought was there must be something wrong with the Fuel Moto map I installed. Luckily for me, Bob @98hotrodfatboy offered to help. I sent him some of the Power Vision data and he noticed that the cylinder head temperature didn't look right. That seemed odd to me, but sure enough, I forgot to re-attach one of the spark plug wires to the coil. I re-attached the spark plug wire and the bikes been running great!
I've put over 16,000 miles since I got the bike back together and the Andrews 48H cams made a huge difference in the low end power, which is where I ride 95% of the time.
A big THANK YOU for Bob @98hotrodfatboy for figuring out the issue I was having. What's wild, is how poorly the bike runs on one cylinder.
I've since purchased the S&S head breather kit for 1999-2017 (900-1299) and the next time I have the rocker boxes open, I'll install them. I wasn't aware of this product when I did the initial work.
I've attached some pictures of the cams and lifters I removed from the bike. Obviously, that was what was causing the engine tapping sound. As members have said on this forum before (and I didn't heed their advice), tappets/lifters are a maintenance item that should be replaced at the appropriate time.

 

Wow that cam and lifter roller look like ****.. You got lucky man, real ****ing lucky.. and thank you for the acknowledgment, I appreciate that very much.. But the most important thing is that you're safely back on the road and the bikes running really good and that's the important thing.. Enjoy man and be safe..