This section is not meant to be a replacement to the FSM.
It is meant as a compliment to the FSM or added information with pics that are not in the manual.
Always buy an Factory Service Manual AND a Factory Parts Catalog to help you along your maintenance path.
The Haynes and Clymer brand service manuals for the most part will suffice and they generally have more pics than the HD Service manual.
But the HD manuals will be the most accurate.
All in all, there are discrepancies in all of them including the HD parts and service manuals though.

• 98 1200S 5 Speed Transmission Inspection
• Known 1991-2003 Transmission Wear
• Setting 1991-2003 Shift Pawl Position
• Why There is So Much Slop in the 1991-2003 Shifter Shaft
• What Causes the 1991-2003 Shifter Detent Plate to Lean
• What Causes the 1991-2003 Shift Drum Pins to Walk Out of the Drum
• What Causes the 1991-2003 Shift Arm to Scrub the Starter Gear
• 1991-2003 Shifter Detent Plate Retaining Ring Alternatives

The original XLF thread was written by Hippysmack of the XLFORUM ¹⁾ and reformatted in the Sportsterpedia with additional information from various XLForum threads and members.
Also reference the sub documents above for a more in-depth look at the shifting mechanism and associated issues with it.
Click on any pic below to enlarge:

Going through all these steps will familiarize you with your transmission both mentally and physically.
Once removed, you should lay the tranny horizontally on a bench and physically run through the gears.
Make sure there is no binding and that movements are free and smooth. It will have some play since it's not installed.
Move the shift forks with your hands to make the gears move and run through and back.

Later on, you'll feel the gear action and you'll know how it sounds and feels when actuated by itself with no load.
This may help you diagnose later when things will not shift properly.

• Countershaft Gears:

Countershaft 5th - 25 teeth

Countershaft 4th - 26 teeth

Countershaft 3rd – 29 teeth

Countershaft 2nd – 34 teeth

Countershaft 1st – 32 teeth

• Mainshaft Gears:

Mainshaft 4th – 32 teeth

Mainshaft 3th – 34 teeth

Mainshaft 2th – 29 teeth

Mainshaft 1st – 20 teeth