The small washer lock is actually a called a push nut. When you get the internal slave cylinder out you will see one holding the cylinder on an index pin to keep it lined up. The small pin holds the inlet line from the master cylinder into the slave cylinder. There should also bee two small O-rings in a plastic bag which ar put into the slave cylinder before you reinstall the hydraulic line. Then you use the lead pin as you describe it.
Hope that makes sense if not when you take it all apart be slow methodical and keep all parts you remove you will find a use for all the new ones. Hopefully you also had a new pilot shaft bearing which goes in the flywheel.
Read all the directions that came in the box and it will help. If you have problems because there is so much labor involved take a picture of what or where you have the question and post up here. This gang of experts can get you through the process.
89YJ 2.5L TBI, AX-5, NP231 SYE, Tom Woods Shaft, 33" BFG T/As, 4" lift.
AF Jeep Club Tail #184