After the 1st-2nd gear assembly is installed on the mainshaft the 3rd-4th gear assembly is installed next.

The Countershaft detailed instructions are HERE.

Slide the 3rd gear needle bearing down over the mainshaft. Then slide the 3rd gear over the bearing as shown.
 

Insert 3rd & 4th slider assembly over mainshaft. The refrence mark faces 3rd gear. The short side of the slider hub faces 4th.

Install Input Shaft Spacer. Note: This is one area you will need to check for endplay.
Different Input Shaft Spacers are available from Ford if needed.