There is a torque spec for the nut on the rod. I have a different loader, but it was pretty easy to find a repair manual on line. I have redone six cylinders on my Kudota loader and backhoe, so far. Do not try to remove the rod by blowing compressed air into the port. The rod can come out like a shotgun slug. Fatal if you are in its path. Check the rod for straight. I had one that was bent. Swapped a "gather" cylinder for a stabilizer cylinder, since the gather rod gets a lot of use and stabilizer only now and then. The bent rod will likely cause a seal to leak, but not for a long time. BTW, the two cylinders are identical, so a swap was no problem. In torqueing the nut, I reinstalled the rod in the tractor to hold it still. I put the pin through the eye and onto the tractor. Works like a vise, but in my opinion, better. It helps me pull out a stubborn rod, too.
I crack open all my own cylinders. Bought an adjustable tool that fits the two holes on the end cap. Some of my cylinders had a soft steel square piece that you roll into a groove as you tighten the cap. Mine were so dirty, I couldn't find them on the cylinders until I cleaned them up real good. Bought the Kubota used, and it wasn't in the best shape when i got it. But I use it all the time now. Don't know how I got along without it. Good luck. BTW, it helps if you get the rebuild kit before you pull yours apart. That lets you know what all parts are being replaced and gives you a clue about how things come apart and go together. That's how I found out about the square retainer in the end cap. The cap didn't unscrew, just kept turning and turning. Once I cudgeled out the retainer, it came right apart.