Correcting the confusion.
Swapping a 5 speed to a 6 speed, things you'll need to change.
Crossmember; needs to be the wide pad version from 1998-2002.
Isolator support on transmission, works from 1999-2005 NV5600.
Isolator, 1994-2002 5 or 6 speed.
Shifter tower (shifter assembly) NV5600 only 1998-2002 (2nd gen).
Flywheel w/revised ring gear, typically a 2001-2002 (2nd gen) piece, but the aftermarket has a wide variety of choices.
Starter spacer, moves the starter ahead on the block plate ~ 1/2 inch, OEM can be either phenolic or aluminum, aftermarkets are aluminum.
Clutch, the later (2001-2005) NV5600s use a 10 spline by 1-3/8" input, typically an OEM NV4500 uses the 10 spline by 1-1/4 clutch.
This is just to mount the transmission in, there also may be driveshaft differences.
Mark.