I installed the 997 shifter today using the B&M instructions. Only screw up was I tore a small piece of the leather on the parking brake lever while taking out the console. Anyway, it's a noticeable improvement over the stock shifter. I like it!
when I installed 997 shifter, I made sure that the transmission was not in any gear, kept the green clamp holding the shifter in place and just dropped the cables into the craddle.
I think marking the cable is for aftermarket short shifters without the centering clamp.