Time to rebuild one of my tractor cylinders. The rebuild kit cost about 100$. To take it in and have it rebuilt would run me 250$. That would be 1k for all 4 so it was worth it to do it myself.
This is the second one I've rebuilt so I'm an expert now.
Seriously though I'm no expert on anything just a guy who hates to pay anyone to do something I feel I can figure out.
All makes of cylinders are different but the basics are the same. This cylinder is a John Deere ( as if the green didn't give that away.

First thing is to remove the external snap ring. At this point u will want to extend the ram. Beware oil will shoot out of the pressure line connections so have a bucket ready.

Now take a punch and tap in the piston/seal retainer.
If u do not extend the cylinder before this step the retainer will block the oil feed line hole and you will not be able to move the piston/rod.

You tap it in far enough to acces and internal groove in the housing.
Clean the internal groove up just to get any crap out of it.

Now in ur rebuild kit there is a plastic ring which fits perfectly in the groove u just cleaned up. Use two small screwdrivers to line up and snap the ring in place. This ring allows a large snap ring to slide over the groove. This groove and snap ring is what keeps the cylinder from just popping out.

Note. If u destroy the removal ring u have to buy a new seal kit to get another one. U can use quick set epoxy to fill the groove if u destroy the orange removal ring.

Once u are sure the ring is in the groove perfect yank the cylinder right out.
Easy peasy

I'll reassemble it today. Stay tuned

That's similar to doing the oddy rear shocks.
You have to press down the top piece (the one with all the seals) with a clamp so that you can get at the internal snap ring that keeps it all from popping out. A real pain in the ### because very little room to work. The trick is to push that snap ring down (very little) to get it out of the groove. Then you can hook it out. That groove is actually beveled on the bottom side but is square at the top, so you will never get it out pulling up. You must push the ring down a bit.

With regards to your cylinder there, I would hone it with a three stone before you put it all back together.
That's what I did when I rebuilt my buddies two post car lift cylinder.

Loctite that nut.

Finished it up first thing this morning. Honeing is not necessary on mine. It is a low hour tractor had 150 hours 3 years ago when my hour gauge went out and I've owned it about 13 years. The outer seals are what fails for me and that's due to age not use. Now then many heavy use high hour cylinders need the shaft micro polished and the inside of the cylinders honed. Many times this is caused from not regularly changing the hydraulic oil filter. And crap in the oil will eat a cylinder over time.
I assume u micro polished the shafts when u were done Honeing.
No thread lock for me. That nut is torqued on plenty tight. Took a 4' cheater pipe on the breaker bar to Crack it loose.
Sounds like u maybe should try the epoxy in the grove trick, Sounds similar to mine. My inner edge is beveled and the outer edge is not. The orange ring takes up the space and the ring allows it to slide right over it.

to remove the nut requires one end to be in a vise and a breaker bar with a 4' cheater pipe. In the second picture u can see where the seal failed.

Seal cartridge " for lack of a better term " prior to cleaning up

These are what they call the external seals. They are a stiff plastic and u must force them in the cartridge which is difficult the first time u do it because the way you must almost crush them seems like it would destroy them but they pop right back into shape. Was easy this time because I knew I would not damage them.

This seal is a hard fiber/plastic material and the best way to remove it is to cut it with an EXacto knife. If u try to dig it out you may damage the housing as its aluminum.
To reinstall the new one u boil some water and put it in there just a second then fight like hell to get it on. There is an O ring under it.

That's about it. Just be sure to lube it well before reassembling.
Total time was less then 2 hours and that included looking for tools ect.
Note that there were two more o rings and another seal but they just pop right on so I didn't bother mentioning them.

So if u are wondering about rebuilding ur own cylinders just know u can do it.

We farm so almost everything we own has a hydraulic cylinder on it. We used to fight those seals that go inside the end cap of the cylinders until we found a tool. (A damn expensive one but worth it) to shrink those seals and they pop right in.

Yup that's called a wiper.

By the looks of those pics I would say your system is contaminated or the filters are not working or it could be condensation from sitting.
You may have over heated it as well as it looks like that one o-ring is cooked but I may be wrong. Hard to tell by that one pic.

I figured they had to have some special tool however I could not picture it in my head.
Im sure it's too rich for my blood since I don't do many of these but I think seeing the tool may aid me in the future.
Thank for the pic.

Farmers feed America. Thank you.

Oil system is clean and so is the filter. The only damaged seal/Oring
Is the one pictured.
The rust crap on the seal cartridge is on the outside of the Oring which seals the cylinder. Had that of come from inside the system you would be correct,my oil would be just a tad dirty.

They say to replace them in pairs but my $$ dictated I do them when I can. The other one went out about 6 months ago and I've been waiting for this one to go.

Some things just wear out over time. No big mystery here. At least not in my opinion.