So what led me to a master cylinder swap was actually just me being stupid and making assumptions that were incorrect. After i did my swap i had very little pedal. Bled and bled and bled the system and couldn't figure it out. I just assumed that with the discs in the rear now my master cylinder wasn't pushing enough fluid and with my proportioning being set up for drums in the rear it was off. When i finally swapped out my MC i had the same problem and it turned out my calipers were no good. So my final say is that an MC swap is not necessary for the discs but if you have access to a ZJ setup its a pretty straightforward swap so if you're up for it swap it in. First i pulled out my MC and discovered that the ZJ MC was a little different setup. I'm sure that its possible to make the ZJ MC work with a YJ booster but i just decided to swap boosters too. The ZJ booster was dual diaphragm which gives you more assistance for the larger bore MC.
So if you're doing the MC swap as well obviously don't worry about bleeding your brakes when your done as you have to disconnect all your lines again anyway. You can either take the lines off the proportioning block or from the MC and reuse your proportioning valve. I don't remember which i did, i think i reused my block.
Once all your lines are off go underneath your dash and go to the top of the pedal where you will see a clip holding the actuator arm onto your brake pedal, undo that and now you're ready to remove the booster. take the vacuum line that goes to the booster off of the intake and unbolt the 4 nuts that hold the booster onto the firewall.
This is the point at which some fabrication comes into play. Basically pushrod on the ZJ booster isnt long enough to reach the pedal on a YJ. Sooo, you have to lengthen it. What i did was cut about 4 inches off of my old YJ booster pushrod and just the tip off the ZJ booster. I used a die and cut threads onto the end of the ZJ booster pushrod, i don't remember what size though.
Then i found a long bushing whose inside diameter was the same as the outside diameter of the peice i cut off of the YJ push rod (getting confusing enough yet?) I welded a nut that matched the threads I cut onto the bushing and then slid the YJ rod into it.
Theaded that onto the ZJ booster pushrod. I mounted up the booster separately from the MC as it was easier to adjust the throw of the pedal like that. Once the new pushrod is coming through the firewall see how much longer or shorter it needs to be to hold the pedal out all the way, a YJ brake light switch works in opposite of alot of other types, when you push the pedal is releases a switch that then sends current to the relay whereas alot of others depress a button as you step on them. So the point of that is that the pedal must be all the way out otherwise your brake lights will be forever on. I used washers to shim my rod but you can find the difference and then weld it or thread it all the way out of however you please, it really doesn't matter too much, just so long as it works.
Once you get your pedal all set just go ahead and bolt the MC up to the booster, hook up the vacuum line and connect all your brake lines (make sure you get the right ones in the right spots) and bleed. I suppose it may be better to bench bleed the MC but i did not and it works fine for me.
Now that i swithced over to the new booster and MC I can lock up my front tires (32's) no problem on pavement, i don't think i could do that with my stock setup with stock tires.
If you need any more info or pictures of anything in particular just let me know. I know the second half of this was a little scarce on pics my internet just got very slow and i got tired of uploading pictures. Post up if you want more or certain things, ive got a lot of them.