I should stress before anything I say that I am no expert. Looking at this objectively, you are describing a situation where the left-right position of the gearstick is not generating the correct positioning of the shift to engage correctly with the appropriate gear. This equates to movement of the gear selector in the vertical plane into / out of the gearbox, movements generated by the bell crank translating horizontal fore-aft movement of the left-hand (as seen standing in front of the car looking down onto the selector) cable into vertical movement in and out of the box - suggesting that this cable is slightly out of position.
This probably excludes adjustment of the cable that rotates the selector shaft clockwise / anticlockwise (equating to fore/aft movement of the gearstick between odd and even gears) assuming that you are able to shift without inhibition between 1st / 2nd and 3rd / 4th even if the gearlever head is slightly displaced compared to normal.
What happens if you put everything (gear lever and box) into the neutral position, and disengage / re-engage the clamp on this cable without doing anything special? I found that this sufficed to sort out a very notchy change on my newly-fitted PTW box (out of haste due to sudden rainfall rather than by design) so that it is mechanical-feeling like a normal Tdi gearchange rather than being overtly difficult - a millimeter of cable adjustment can sometimes give substantial benefits.
