how to adjust shift linkage?
 

After doing my clutch i notice going in to second gear is kind of rough, how do you adjust the linkage?

1. Get a new shift lever and White plastic cup under shift lever.
2. Tighten carefully all linkage bolts by the transaxle.
3. Check to see if your rear linkage is per Clarks

Transaxle - Checking, Repairing, and Replacing the Shift Lever and Shift Linkage

If the white plastic piece on top of the transaxle is worn=NLA Bottom picture in link.
I have used thin shims to improve shifting on the "intermediate shift lever"

Your shift lever may have deformed the hole in the shift rod. Again you can shim.
If so, link available.

GL
John