Update... hopefully the final:

Did what I did, was suggested above and she's happy now. Cough is still there but only 2 times while the engine was still cold. Performance is back to normal! The only thing left is the fine tune up of the mixture setting. So, here it is gents, tell me what you think? RPM, rich vs lean? (I think it's still running lean):

 

It was the intake manifold gaskets?

 

Most likely. I also put back the original vacuum slide

 

Check your spark plug color. Good work!

John

 

Brand new plugs, this is after about 150 miles yesterday. A bit on the lean side?

 

@npn you have patience my friend!

 

That's an understatement

 

Final update and lessons learned

The bike is now happy. All I did is lower the idle rpm to the liking of mine when it was hot. Have taken it twice for a hard ride and the idle is fine; took it to over 80 mph on a stretch too and when I got to a stop light, the engine was idling beautifully. So I don't know, maybe after it got hot a few times, the seals adjusted/set properly. Then at home I put the Tachometer on and it was oscillating between 930 and 960. I know, a bit on the low side but I'm done fiddling with it.

As far as lessons learned, I'm not sure if I would change the intake seals, and in my case, the intake manifold itself. Remember, the biggest complaint I had was a random cough or two in the first 20 minutes of each ride. Really, if it ain't broke, don't fix it. The only thing I needed to do is change the original set of jets. 23k mi on this bike, original, virgin carburetor that imo had never been serviced and it was fine; besides the burn residue it wasn't plugged or contaminated in any way, which to me is a testimony of Harley's design/setup, and that, my friends strengthened my respect for this brand and I'm on to my search now for a used RK so the missus can enjoy my rides too!

Many thanks for all the people who chimed in responded to my questions with the same passion as mine! Cheers

 

Yep, they look like the Cycle Shack pipes from years ago. Great pipes, and you cant buy them anymore. They stopped making them back in the late 90s or early 2000s.

 

Those tubes are for the heads to breathe. The factory routes them into the carb and the motor sucks it in and re-burns it. Most people re-route them externally to a catch can or to the ground to keep that garbage out of their motors.
Google Harley external breather, theres tons of videos and posts on how to do it.