Yeah, from messing with mine over the time I found the best way is really just to treat the pin/screws as lock outs really.I did the "adjustment" with the pins, at the shifter. But I was too lazy to mess with the cable ends at the transmission. Very notchy (in a good way, to me) but I should probably do an actual adjustment at the transmission.
The turnbuckle one can adjust the side to side throw preference though.
With the side to side adjustment using the end links you really just disconnect the tension or Allen bolts on the endlink will the shifter is in neutral or 3 or 4 gear, then tighten that up and your side to side is now perfectly aligned and you just have to set the pins for the locking the distance needed to get into 1/2 and 5/6 gates(I think just 5 in your case)
Front to back is really just for user preference of the location that you like the shifter at for neutral.