Some 6 spd users have to trim the inner boot for shifter clearance with a body lift.
Some also use a zip tie to hold the boot lower on the shifter.
Finally, some go through a process of moving the entire body back as much as 1/8" to 1/4" on the frame. They do this by loosening all the body mount bolts, then backing up in reverse followed by slamming on the brakes a couple times to move the body on the frame.