So, these past 2 days, I have been tackling replacing the clutch in my 06 LJ, only to find that the clutch wasn't my problem, but rather I had a stuck slave cylinder as a result of a broken master cylinder. After much research, it seemed that the only option was to replace the entire Master Cylinder, Slave and all piping as a single unit, as Chrysler calls it a "sealed system". Well I'm here today to tell you that that is a bunch of BS. The entire kit sells for upwards of $200, where my solution will cost you $66, maybe less if you are not quite as strapped for time as I was and you can find the part elsewhere cheaper. Please bear in mind that this solution will only work for you as long as the main "outer shell" of your master cylinder is in good shape. If you are like me, and the shell is fine, but the internals are shot, this will work.
Here are the steps:
First, you will need to source through your local Napa or otherwise, a master cylinder for a 2000-2003ish Dodge Ram. What I plugged into their website was for a 2000 Ram 1500. The Napa part number I wound up with was 72354. The first picture here is the Jeep master cylinder:
Here is the Dodge master cylinder:
These are identical parts, with a few exceptions. On the Dodge, it appears there must be a remote reservoir, where the Jeep one is mounted to the cylinder. When I inspected these two parts closely, they even had the same part number stamped on them. When you pull the one out of your Jeep, near the end where the pipe connects to it, you'll see two small holes, one with a metal pin in it, you need to push that pin out to get the cylinder off the tubing. I used a small punch and was able to push it through far enough to pull it out the other side with needle nose pliers.
Attached to both cylinders, is a metal attachment with 2 studs on it used for mounting to the firewall. This will twist off of the cylinders with a quarter turn. Remember which one is for the Jeep, as they are different shapes due to different firewalls.
Once you have that off, you will see a snap ring inside the end of both cylinders. Using a set of snap ring pliers, pull that ring out. Behind that is the plunger assembly, the end of which looks like this:
Using a pick tool or something else with a hook, you can pull the assemblies out. In my case, here is what my Jeep's plunger looked like:
Now, you just need to swap over the new internals from the Dodge piece into your Jeep's cylinder. Put the plunger in, and then replace the snap ring behind it to keep it from coming out of the cylinder. There is a gasket that goes between the metal piece that holds the cylinder to the firewall and the cylinder itself, make sure to put that on (I used the new one from the Dodge part so I had all new components) before putting the metal part on, or it won't stay together right. Make sure at this step you pay attention to the correct orientation of this bracket in relation to the holes in the firewall.
If you removed your master cylinder from the Jeep with the arm from the clutch pedal, and neutral safety switch attached like I did, you'll want to put these back together now. In the Dodge kit, there is a new off white colored plastic washer, and a foam washer, these go on the arm from the clutch pedal, in the following order: Neutral safety switch, plastic washer, foam piece. Here it is assembled in my Jeep, I tried to pull the nss out of the way as much as possible so you can see it:
At this point you can push the arm and switch wiring back through the firewall and re-attach the cylinder to the firewall, and the neutral safety switch wiring and arm to clutch pedal. Now once you have re-attached the piping to the rebuilt cylinder, (there is a new metal pin in the kit, or your can reuse yours if you didn't lose it), you can bleed the system using the method outlined in this thread.
Note, that between my writeup and the one I just posted, you should be able to fully replace either the slave or master cylinder, instead of buying the whole kit just because one of the two went bad! I hope this helps someone, it caused quite the headache for me, and due to other repairs already in progress on my Jeep, I really didn't have the money to replace the whole system.