i got lazy & didn't read whole thread, so excuse me if this was mentioned. but did you ever check the master cyl adjustment?

from the symptoms you described it sounds like the clutch is not disengaging fully, its an easy fix, you just need to adjust the release point.

follow the pedal assembly up under the dash, slightly behind & above the clutch switch you will see a threaded rod with locknut that attached the master cyl to the pedal assembly, this usually needs a small amount of adjustment when installing an exedy twin to get the clutch to release fully. if that doesn't work id suggest bleeding the clutch line incase there is a small amount of air in the line as this will have the same effect/symptoms

 

All his gears are fine... except there is no sixth. Dont think thats clutch related...

 

Find out the name of that part and I will give you the part number, if it is the clip.

 

the OP states that 6th was fine before the clutch install as well the mentioning that it is "popping or "clicking" when going into some of the other gears now, clear signs that the clutch is not fully releasing & in need of adjustment

 

This is my theory on this issue pay a real expert to install your clutch next time..