After the Mainshaft and countershaft have been installed in the case the 5th and Reverse assembly is next.

The 5th and Rev detailed instructions on disassembly are HERE.
The 5th and Rev detailed instructions on assembly are HERE.

The locking nuts are "staked" to prevent the nut from backing off. Below the pic shows the two locking nuts.
The mainshaft & Countershaft nut had to be ground around the threads for removal.

Depending if your trans has been rebuilt you may have to work extra hard to get the locking nuts off.
The last rebuild of this trans the rebuilder did not have the proper tool to torque the nut so her used a hammer and chisle.
Please do not use a hammer to remove or install the locking nuts. Lack of the proper tools can cause you to damage the trans.
One or two hits from the stake is all that is needed to lock the nut in place.

After the Counter and Mainshaft are installed with new bearings the rear bearing plate is installed.
The rear bearing plate must be installed first before you will be able to check the front bearing clearances.

Refer to the shop manual for proper shim selection.
If you cannot get the OEM shims then the aftermarket sells shim spacers.

Insert the ball bearing into the countershaft and slide the 5th gear sleeve over.
Note: A small amount of grease will help hold the ball bearing in place.

Improper shiming of the Front bearing will cause damage to the rear bearing retainer plate as shown below.

This trans did not have the proper front shim which allowed the bearing to rotate and cut the rear bearing plate.

For exact assembly of the 5th and Rev assembly please refer to the OE shop manual.
Note: Be aware this trans has three ball bearings and they are different sizes. Bag and tag each ball bearing.
Installing the wrong ball bearing in 5th gear can cause problems.

Check thrust washer endplay on Reverse Idler Assembly.
The Reverse Idler detailed instructions on installation are HERE.

Install 5th and rev assembly per shop manual installation instructions.

Countershaft needle bearing install.

For proper endplay check with feeler gauge and refer to the OEM Shop Manual for the proper split washer selection.

Installing the Mainshaft bearing using the Autozone exhaust pipe again.

Install the two locking nuts and torque them the the proper specs. Then stake them as shown below.
Note: The mainshaft locking nut will require the proper tool to torque the nut.
The socket and extension tube costs almost $275 so a quick trip to your local Ford dealer maybe needed.

Speedo Gear shown with snap ring. A ball bearing is under the gear so be aware of it.

Click on pic below for large image.

Here is a damaged Reverse gear caused by incorrect thrust washer.

Teeth worn down. Ford no longer sells this part you can get it aftermarket.