The synchronizer assemblies have alternating high and low areas on the friction rings and clutch rings (Fig 21).

When assembling the single-cone synchros, make sure that the high area on the friction ring is seated in the high area on the clutch ring. 

On the dual-cone 1-2 synchronizer assembly, be sure you have the high areas on the friction ring seated in the low areas on the clutch ring. If they aren't assembled correctly, the synchronizers won't work, resulting in gear clash.

Another item to watch for during assembly is shift arm position at the primary shift rail. Be sure the match the position you noted before disassembly. The shift arm closest to the geartrain should be for reverse. Moving out from the geartrain, the shift arms should be for 5th and 6th gear, than 3rd and 4th gear, with the 1st and 2nd gear shift arms being furthest from the geartrain (Fig 22).

Using the appropriate special tools, install the bearing races for the input shaft and countershaft. These races are installed above the surface of the clutch housing to ensure shim clearance. 

Because the mainshaft and countershaft endplay and adjustment is critical to NV5600 operation, we'll look at the procedure in some detail. Remember to consult the service manual for complete instruction. 

Before making endplay measurements, rotate the mainshaft several times to seat the bearings in the races. Measure the main and countershaft endplay with special tool C-3339, which is a  dial indicator set and special tool 8161, an extension rod (Fig 23).

The measurement is taken at the rear of the transmission, and the proper endplay for the mainshaft and countershaft should be 0.002" to 0.006" (0.051 to 0.150 millimeters).