Hi,my clutch pedal is moving from side to side about 10mm at the cotter pin pushing the master slave cylinder rod off centre. Also stopping pedal returning up. Any idea how to fix this?

Hi there if clutch master and slave cylinders are operating with full pressure and clutch fork push rod moves to full release, Then clearly the problem points to a faulty clutch specifically pressure plate or damaged clutch fork.

1995 YJ if still stock all that is ONE PART, see FSM quote below.
is the fluid dropping, day by day, week by week???
y/n?
yes, then either the slave or mc are bad.
sometimes both can fail, (rust happens inside and is progressive)
what I do , is this. (if not wanting to change out both)
1: look at the MC, if it done leak down either side of the fire wall
it might be good (dont mean the piston seals good but its not leaking, so if fluid drops , (every week say) the the MC is ok
and for sure the slave leaks.

2: so where is your slave. have you looked,? (swaps happen)
most leak and can not be detected as that leak landed on the road to work.
for sure its just 2 parts, here, you know the clutch is ok.
because it works with fluid in the system and bled.
now ILL PASTE THE FSM words out of a real factory service manual.
they are clear.
FSM words, QUOTE:
CLUTCH HYDRAULIC LINKAGE REMOVAL
The clutch master cylinder, slave cylinder
and connecting line are serviced as an assembly
only. The linkage components cannot be
overhauled or serviced separately. The cylinders
and connecting line are sealed units. Also
note that removal/installation procedures for
right and left hand drive models are basically
the same. Only master cylinder location is different.
(1) Raise vehicle.
(2) Remove fasteners attaching slave cylinder to
clutch housing.
(3) Remove slave cylinder from clutch housing (Fig.
9).
(4) Disengage clutch fluid line from body clips.
(5) Lower vehicle.
(6) Verify that cap on clutch master cylinder reservoir
is tight. This is necessary to avoid undue spillage
during removal.
(7) Remove clutch master cylinder attaching nuts.
Note that one nut is accessible from engine compartment
and one nut is accessible from under instrument
panel (Figs. 10 and 11).
(8) Remove clip securing clutch master cylinder
push rod to pedal and slide push rod off pedal pin.
(9) Disconnect clutch pedal position switch wires.
(10) If pedal pin is equipped with bushing, inspect
condition of bushing and replace it if worn or damaged.
(11) Remove clutch hydraulic linkage through engine
compartment.

The axle job should not have caused any problem to develop in the clutch.
I don't see how they could have.
If you can work the slave by hand, it may be a problem with the clutch master cylinder. Maybe the rod from clutch pedal into the master is bent or binding up and won't travel into the master. You could check if master operates easily by taking line off at the slave cylinder (or if not able to remove hose, then open the bleeder valve on slave) and see if your pedal operates now. Use a can to catch fluid if you don't want it to spill on floor. If the pedal still won't move it must be a problem with the master cylinder or the clutch rod.
If the pedal works with line removed, or the bleed valve open, then the release bearing inside the bellhousing must be binding up and not moving forward to engage clutch. (The slave cylinder pushes the clutch fork lever which pushes the release bearing forward on a shaft up against the clutch pressure plate to allow the clutch to operate .If the release bearing is the problem, the transaxle will have to be removed to fix it.
As I said, though, if you can operate the slave and the cllutch lever it pushes with your hand, it doesn't sound like it is binding down there. Check the pedal's push rod going into the master cylinder. Good luck.

on the transmission there is a slave cylinder that works like a brake cylinder, when you apply pressure to the clutch pedal a rod inside the vehicle under the dash pushes into a clutch master cylinder, (almost like a brake master cylinder without the reservoir, as the clutch master cylinder works off the brake master cylinders reservoir) the plunger in the clutch master cylinder applies fluid pressure to the slave cylinder,(located down on the trans near the clutch fork assembly) which projects a piston rod into the clutch fork dis-engaging the clutch. To bleed the clutch slave cylinder locate the bleeder screw on the slave cylinder,break loose so it loosens and tightens easily. Check fluid in brake master cylinder reservoir,fill if needed, while bleeder on the slave cyl is closed have a helper push clutch pedal to floor and back 7-8 times, (At first the clutch might stay at the floor, just pull it up by hand or foot and continue) after several pumps with no rest time push pedal to the floor and hold down with foot pressure, at this time loosen the bleeder on slave untill fluid leaks out, watch for air bubbles, close bleeder and repeat untill there is no sign of air bubbles, (make sure to check fluid in the brake master cylinder and keep fill as needed, do not let fluid get less than 1/2 empty as it might **** air and you will have to start over) If this does not bring clutch to operate then you need to check if slave cylinder is reachig its full extension of push rod or not. If it is not then you will have to replace the clutch master cyl or the clutch slave cyl or both as seals are bad and wont hold pressure. Or you need to inspect the clutch fork,the throw-out bearing, or the pressure plate fingers and clutch plate for failure or broken bent parts. I hope it turns out to be a easy fix on that clutching thing.

Is you clutch working. block wheels set parking brake don't start.
Have someone push on the clutch pedal. Look for rod to move on side of bell housing. Okay not working.
Check you clutch master Cylinder for fluid.
Fill and pump pedal slow to remove air from system. If this don't work try opening bleeder on slave cylinder attach a hose to bleeder and place other end of hose in a jar 1/2 filled with fluid. Now pump slow pedal very slow. (Don't run out of fluid or over flow jar.) If fluid is black it is 1 sign you may need to rebuild or replace master cylinder or slave cylinder.
If rod was moving you could have a bad clutch. If with engine off can you put it in gear?
If have an ""automatic"" your switch on your brake pedal are may have gone bad.

you may have a faulty clutch master cylinder or faulty clutch slave cylinder- leaking clutch fluid. most of the time both are replaced at the same time which should be recomended by your mechanic, the bolts to the master cylinder are very hard to get to and require the right tool.
you should be able to move car forward by selecting 1st then cranking engine till it starts, gear changes while driving are hard but not impossible. i recommend a tow truck to a local repairer.

a defective master has just one common symptom, a soft sinking pedal.
Instructions Things You'll Need:

• Nose pliers
• Ratchet and socket
• Ratchet extension
• Slip joint pliers
• Wrench
• New cotter pin

Removing the Old Brake Booster
1. Step 1 Park your car in a safe place with enough room to work around the front and driver side of the vehicle.
   
2. Step 2 Locate the booster push rod connected to the brake pedal.
   
3. Step 3 Remove the cotter pin securing the booster push rod pin to the brake pedal using a pair of nose pliers.
   
4. Step 4 Release the push rod pin from the brake pedal and slide the push rod off the brake pedal.
   
5. Step 5 Unscrew the four mounting nuts off the brake booster studs using a ratchet, ratchet extension and socket. You should be able to see the four booster studs extending through the firewall, in front of the brake pedal.
   
6. Step 6 Disconnect the vacuum hose from the brake booster, working from the engine compartment. Use a pair of slip joint pliers.
   
7. Step 7 Remove the two nuts holding the brake master cylinder to the brake booster. Use a wrench or ratchet and socket.
   
8. Step 8 Separate the brake master cylinder from the booster just enough to make room for booster removal.
   
9. Step 9 Pull the brake booster off the firewall and remove it from the vehicle.
   Installing the New Brake Booster
10. Step 1 Set the new booster in place by sliding the push rod and four mounting studs through the mounting holes on the firewall.
    
11. Step 2 Slide the brake master cylinder flange over the two mounting studs on the brake booster.
    
12. Step 3 Start the two brake master cylinder mounting nuts by hand to avoid damage to the threads.
    
13. Step 4 Tighten the two brake master cylinder mounting nuts using a wrench or ratchet and socket.
    
14. Step 5 Connect the vacuum hose to the brake booster.
    
15. Step 6 Screw the four mounting nuts to the brake booster working from inside the vehicle. Start the nuts by hand to avoid damaging the threads.
    
16. Step 7 Tighten the four mounting nuts using the ratchet, ratchet extension and socket.
    
17. Step 8 Position the brake booster push rod over the brake pedal and slide the push rod pin.
    
18. Step 9 Install a new cotter pin to secure the booster push rod to the brake pedal
    

If hydraulic actuated mechanism, loss of fluid, defective master cylinder or slave cylinder at the clutch. Missing pin or other part between slave cylinder and clutch arm. Loose or broken slave cylinder mounting. Missing pin or broken part between pedal and master cylinder. If mechanical linkage, look for broken components or missing pins at moving joints. If you tried to shift into gear with engine running, you may have damaged the transmission gears.

the mechanic should place or connect the clutch pedal spring to the clutch pedal .connect the push rod to the clutch pedal.then connect the push rod to the clutch master cylinder then refill the clutch master cylinder .by means of pressure tube connect the clutch slave cylinder .then connect the clutch slave cylinder to the push rod .And the push rod connect it to the clutch pork. the clutch pork connect to the spring. then connect the fly wheel , the clutch linning ,the clutch disk ,the release bearing,then the clutch pork to the transmission shaft . then connect the transmission assembly.And you can goon with your date.

Stop driving the car now! The clutch master cylinder has an adjustable pushrod, it is set up too long now. Take it back to where it was done and tell them if they don't know how to set up clutch free play, they shouldn't have attempted the job. This may have cost you a $3500. clutch job. Get it adjusted fast.