Hole for shifter cable
Depending on what shifter you have it can go a few different ways.
Some say over the trans and back under it, some say drivers side loop.
Mine goes through the floor and arches up under the headers flange on the head and circles back down to the trans for a nice straight shot to the linkage.
It's pretty easy but don't bother doing it till you can relax and take your time.
I'd bet I snaked that cable in, out, up, down and around 6-8 times before I was happy with it. (All while being really carefull not to kink it)