The following writeup text and pictures are the work of a Mustang IRS pioneer, Joe Lynch. All credit goes to him. I am merely archiving it here.

Original link here

Removing and Replacing the Half-shafts and IRS Differential Pumpkin

It is not really very difficult to remove the Pumpkin from a 99 Cobra. The procedure is just more like that used for a front wheel drive car with half shafts and constant velocity joints (CVJs) than anything else. The ring and pinion gear setup is exactly the same as for a standard live axle 8.8" Ford rear end.

Removing the Half-shafts

Some of the steps in the the shop manual procedure can be bypassed but not the torque settings or other specifications. I used jack stands and a creeper in my garage rather than a lift. The only special tools you will need are a 36mm socket for the axle nuts and a wheel puller (Autozone 27037 shown).

After carefully supporting the car on jack stands ahead of the IRS at the chassis, and removing the rear wheels:

1. With the parking brake on and the car in gear, use a 36 mm socket and a breakover to loosen the large axle nuts. Remove the nuts.

2. Remove the toe-in tie-rod at the knuckle. You may have to use a puller once the cotter pin and the nut are removed. The aluminum end of the knuckle is large so make sure the puller you get is large enough to clear the knuckle arm, if you go buy a new puller at Autozone. I believe the proper puller is part number 25202 and is about 3.5" wide overall. One that is too small is also shown below for comparison.

3. Take the parking brake clamp loose at the spring lower mount on the lower control arm.

4. Remove the nut on the lower knuckle bolt but leave the bolt in place for now to hold the knuckle steady while you push the axle out of the hub. Leave the brake calipers and parking brake cable installed.

5. Install a puller (Autozone 27037) on the wheel studs and push the axle stub end out of the hub. You can get the axle started out of the hub with the puller then remove the lower knuckle bolt and pull the knuckle out and up to get enough clearance to get the axle completely out of the hub. Leaving the lower bolt in as long as possible just helps support the heavy knuckle/brake assembly while you are wrestling with the wheel puller. When the splines are clear, raise the knuckle assembly up as high as possible and push the axle completely out of the hub. There is just enough clearance to get the half shaft stub axle out of the hub from the inboard side. Lay the half shaft down on the lower arm and lower the knuckle. Put a jack stand or some other support under the knuckle assembly if you can to keep it off the half-shaft.

6. Repeat on other side.

(Go to step 9 now if you are just changing out a half shaft. No need to remove the exhaust or the ABS sensors unless you are pulling the pumpkin.)

7. Remove the cat-back exhaust system now to allow access to the pumpkin and half-shafts during removal.

8. Remove the ABS sensors with a 1/2" open end wrench or the proper Torx head socket.

9. You can gently pull the half shaft inboard stub shaft from the pumpkin. Nice but not necessary to have two people, one to support the inboard stub shaft and one to support, pull the other end of the half shaft. Before removing the half shaft, note the clearance between the ABS sensor wheel and the pumpkin case for reference when you put the axles back in. Just support the inboard stub shaft and carefully pull it out of the seal and support bearing in the pumpkin.

All that is retaining the stub shaft in the pumpkin is a Circlip on the axle which fits in a groove in the spider gears in the differential. When these are new and not corroded, it takes very little force to overcome the slight spring force of the Circlip in the spider gear groove. If needed, you can use a screw driver at the pumpkin but the shaft should come out very easily without much prying. Leave the half shaft lying on the lower control arm. You don't need the special tools in the shop manual to remove the half-shaft.

Just be careful putting the half shaft inboard stub shafts back in the pumpkin. Oil the stub shaft where it runs on the seal and put them straight in. It helps to have a helper support the outboard end of the half shaft when re-installing the inboard stub shaft. Make sure the shaft goes into the pumpkin all the way and that the Circlip re-engages the groove in the spider gear. You will feel it click into place and the clearance between the ABS sensor and the pumpkin case will be the same as it was before you removed the half-shaft.

Reverse steps to re-install. Clean the hub splines and use antiseize before re-installing the half
shafts so they will be easier to get out next time. Use antiseize under the axle nut, too. Get the axle nut as tight as you can--spec is 240 ft-lbs. The book says use a new nut. I didn't, you decide. I checked the nuts a few weeks later and it was still tight.

Do not tighten the lower knuckle bushing nut until you put a jack under the lower control arm and raise it back up to the normal ride position. If you tighten it with the lower control arm at its full extension and then lower the car, the bushing is restrained at the jacked up position and gets twisted way too much when the car is lowered and the bushing may become damaged, according to Ford.

Pumpkin Removal--After Half-shafts Are Out

Do not remove the brace under the yoke. It can be left in place. Match mark the drive shaft and yoke and drop the drive shaft. Leave the drive shaft front yoke in the transmission. Remove the two front pumpkin support bolts using 18 mm socket and box wrench for backup. Rest the front of the pumpkin on the cross brace. Then put a floor jack under the pumpkin and remove the two
15mm headed rear bolts. Have friend slowly lower floor jack while you tilt front yoke up to clear
the front brace. And lower the pumpkin to the floor, keeping it level horizontally so that the lube
doesn't run out the axle stub shaft holes.

Reverse to re-install. I put the 3 pints of lube in before putting on the rear cover. I also used
antiseize on the outboard stub shaft splines and the axle nut to make it easier to disassemble next
time. Also used antiseize on the drive shaft bolts and mount bolts. None on ABS sensors since they
had loctite on them from the factory.

There is no gasket on the pumpkin cover. Just a groove for RTV sealant.

Edited by Postban to add: TA31 is the Ford number for the Diff sealer. I have also had Permatex Ultra-Grey work equally well.TA31 is $15 per tube, Ultra-Grey is $4

I used a professional shop to set up the ring and pinion since I don't have a press for the pinion
bearing.

Torque Specs in Ft-lbs and Wrench Size

Rear axle nut--------240---------36mm
ABS Sensor-----------17----------T40 or 1/2"
Tie Rod end----------35----------18mm
Shock Lower----------98----------18mm
Knuckle Upper--------66----------18mm
Knuckle Lower--------85----------18mm
Lug Nuts-------------95----------13/16"
Diff Housing Cover---24----------13mm
Filler Plug----------25----------3/8" square
Pumpkin Front--------52----------18mm
Pumpkin Rear---------76----------15mm
Driveshaft-----------83----------12mm 12 point

Joe Lynch

The above writeup text and pictures are the work of a Mustang IRS pioneer, Joe Lynch. All credit goes to him. I am merely archiving it here.