I'm a little confused from instructions and about to start shifter install. Do you install shifter on bench on after the box is in the rig?
You can but be sure to leave it loose. It might take some finessing to guide the shift levers into the cab as the case is raised. with a BL & a TT, it was tight but I did the following:
1. installed the shift levers on the shift tower and left it on the bench
2. Insert the full length 1/2-13 all-thread and jamb nut into the case and install into the vehicle. Pull the rear axle shift rail out so the case is in high. On the case, this one is on the drivers side.
3. Thread a spare 1/2-13 nut onto the all-thread then slide the shift tower (with shift levers attached) over the all-thread and guide the shift levers into the cab.
4. AA says to start with the rear shift lever. I went back in the cab and re-installed the console and taped a 19mm, 1/2" drive socket to the shift lever acting as a "guide". It centered the shift lever in the console opening and left about 3/8" to the back. a quick-clamp holding the shift lever to the console acted as another set of hands. Following, under the vehicle, I adjusted the spare 1/2-13 nut so the shift rail was close to the top of the case, per AA's instructions.
5. Make your 3/8"-24 link for the rear (leave a bit long). It's only for fine-tuning.
6. Shift the rear into low
7. Place front axle shift rail into Neutral
8. The socket taped to the rear shift lever helped act as a "spacer" to set the front shift lever location
9. make your shift linkage for the front.. Leave it a bit long.
The above is a good starting point but fine tuning will be needed. After it's found a "happy place" and you're 9 beers deep, 12 helps, and you're good with it, measure and cut your tower extension tube. Disassemble and re-install with the cut tube, minus the spare 1/2-13 nut. Trim the 3/8" and 1/2" all-thread to their final lengths. remember to cut the shrink tube an extra 3/8"-1/2" long and I put loctite on everything.
Good luck.