For closure of this thread, i want to post what actually fixed my tranny problem.
I took my truck to a reputable tranny place. They diaganosed my truck and came back with two issues,
the clicking was a broken fly wheel.
the speedometer bouncing, erratic hard shifting was caused by a bad speedo drive gear in the rear of the transfer case.

they replaced both, repaired muffler, and installed helicoils and my truck needed. It now runs smooth, shifts great, speedometer works.

The reason I took the tranny issue to the shop is because they were going to help warranty my tranny with junkyard, they came back with the afformentioned issues.

I feel like i was so close to solving it on my own. I did replace the speed sensor and inspected the gear inside but I wasn't sure what I was looking for in damage. Apperently a code helps diagnose this issue.

Im surprised about the flywheel clicking being inconsistent and not worse at higher speeds.

In hindsight, the inspection of the flywheel during a tranny install is very important.

Hope this thread helps someone in the future. thanks everyone for helps and comments.
my truck is running now and will slowly build confidence as I use more....