Most shifting issues can be related to an improperly adjusted shifter, or tired, inatentive shifting.
I also see a lot of shifting "hard shifting" or "difficult shifting" complaints within the first 2000 miles.
All those trans parts, just like your engines, need to break in, wear to each other and learn to slide around together.
This is also why I encourage using a synthetic, heavier weight oil in the trans like a 75w90 GEAR LUBE, ( I use 75w140 Redline synthetic heavy shock) instead of thin, motor oil.
The heavier viscosity numbers quiet a lit of clunking and normal trans noise, and the synthetic aids in shifting and smoothness.
“When the going gets weird, the weird turn professional....” ~ Hunter S. Thompson~
R.I.P. Rubberdown. 1971-2012
"Your Jedi Mind tricks will not work on me...... ~Misinlink-2016~
2005 E.G. Classic
S&S 510 cams
Baisley Oil pump spring
Rinehart 3.5" pipes
S&S adj pushrods
3 stickers (Adding 5 hp each. I swear......)