With the trans in place, mark the floorboard and cut it just large enough so there is room to bolt the shifter and linkage to the trans. Once they are bolted in, you can set the hump loosely in position and figure out where it needs to be so that the hump fits the floor and the shifter can go into all gears w/o hitting the opening in the hump. Don't think you'll have a lot of leeway as to where to put it so the shifter actually works, but it won't hurt to make sure the hump clears the seat, too.