If Jerry can(not) still modify the 4MT cross-members to fit the 5MT - this I don't know. But last time I talked to him (10+ years), his phone number was 5o9-nine5two-2eight5five.
The 5MT swap process is relatively straightforward. Transmission, clutch kit, clutch fork, and flywheel come from the 85 to 89 5MT dual range. You can have a single-piece driveline made, or make a mount for the 5MT center carrier. Jerry's cross-member is simply a modified 4MT cradle with 5MT mounts on it. The 4WD linkage rod has to be lengthened by 1", and will otherwise bolt on. The 5MT gear shift linkage needs a mounting point (stud or bolt) fitted to the floor pan to hold up the back of it.
It's been done hundreds of times. I've personally done probably 15-20 of them. I have Brat at my shop right now that's got an EJ22 and an XT6 full-time 4WD 5MT in it. It's all actually really simple.
4MT's are hot garbage. Put no effort toward them. It will be wasted.
GD