There are two adjustments that are important, and one affects the other.
First, see if the toe lever is where you want it, comfortable for your foot position.
Now look at the arrangements of the two levers the tie bar is attached to. One from the tie bar to the transmission shift shaft, the other (part of the shift pedal) from the tie bar to the foot pedal pivot point. Those two levers should be as close to parallel as you can get them.
Sometimes you have to remove the transmission lever from its shaft and rotate a tooth or two on the spline, then readjust the length of the tie bar for your foot position. Sometimes readjusting the tie bar length moves the levers out of parallel again and you have to try again. Usually two tries at the most will get it right.
When you went to reinstall the shifter on the shaft, did you removed the pinch bolt entirely so the shifter slides all the way back on the shaft? Otherwise it only goes on about 1/4 inch, and it could twist and cause rough/clunky shifting.