My wife's 2001 4-runner, she has had since college, needed some suspension love. A little history. When I met her, "the car" she had 135,000 miles on her. She was burning oil and just in rough shape. I got a JDM engine for around 1000$ and swapped it out for the old. The JDM had 55k on it. We now have 175k miles and its been running like a champ. Since its been doing so well I decided to spend the money getting it all up to snuff. Finally plunked down for OEM inner/outer tie rods, OEM lower ball joints, Energy suspension bushings and bump stops, KYB struts and shocks, and a couple other little items.
This will walk through my experience replacing the inner and outer tie rods and lower ball joints. It was pretty easy thanks to no rust and PB Blaster.

First things first, break lug nuts free, jack up vehicle, place on jack stands and engage E-Brake to prevent movement and chock wheels. Remove wheels. Spray down bolts with PB Blaster if you havent already.
I like to break all my bolts free first and then start disassembly. I started with the castle nuts on the OTR and LBJ. Of course you must remove the cotter pins first. Don't be cheap, put new ones in.

Next, break the 4 x 14mm bolts holding the LBJ to the LCA.

Then break the lock nut on the OTR. I used a pipe wrench to hold backup.

If you haven't removed the clamps on the dust cover do that now. I found it easiest to pinch the tabs with pliers and use a flathead screwdriver to pry up the metal lock. I didnt damage it but had a new one any way.

I wanted to remove the ITR and OTR before I removed my LBJ. I used a 3 arm puller to pop the OTR out. I compressed them until I felt they were putting sufficient pressure, then used a hammer to shock it into releasing. Watch your hands!

Then I marked the OTR where the lock nut to help with installation. See the yellow paint? Count your turns on removal, mine was 19 on passenger side and 18 on drivers side.

You can now remove the dust cover.
We are going to bend the lock washer tabs back on the ITR. I used a flathead screwdriver and hammer. There is a new washer with the new ITR.

Then I used a pipe wrench to loosen the ITR. There are flats behind it you can place a wrench on to hold backup. See above pic.
Now that the tie rods are out of the way I used the 3 arm puller to pop the LBJ out.

Then you can remove the 4 mount bolts and remove the LBJ.

Installation is basically the same as removal. A few tips.
When installing the LBJ, use a small jack to raise the LCA into the ball joint stud. Torque is 105 lbs on the castle nut. I don't torque anything until the end though.

After you have hammered in the washer to the flats on the ITR you can install the dust cover. The dust cover goes to this groove on the ITR. Meaning the front of the cover will just hide the groove. Please put the clamp on before you install your OTR or you will have to take it apart again. Ask me how I know.

The torque on the OTR castle nut is 64 lbs.
The torque on the LBJ nuts are 54 lbs.
I don't like to torque anything with the steering rack locked, so put the key in ignition and move the wheel until it stops and torque it up.
Don't forget to have your alignment checked.
Hope this helps someone.