the 6-speed transmission is longer than the 5-speed. you´ll need a shorter rear driveshaft if you don´t have an SYE with a CV driveshaft. the front driveshaft should handle this difference.
all mount points are the same. everything should fit. only the whole drivetrain will become a bit longer.
we did such a tranny swap on a friends TJ. (5-speed manual to 3-speed auto)