I moved the linkages around while fiddling with my shifter before install too. To get a general idea of where they need to be, I marked where each shifter cable was for each gear with a sharpie before removing the stock shifter and adjusted the linkages on the Coolerworx to match after install. This also helps with setting the stops for R, 1-2 and 5-6. If you don't mark the cables it's not a big deal either; adjust the side to side cable linkage so it goes into 3-4 easily when centered. The front to back linkage doesn't matter as long as it doesn't bind up, you can set it where you want to move the knob forward/backward.