If you got the gland off that easy (and we KNOW the piston nut wasn't on very good) then the cylinder likely wasn't assembled correctly in the FIRST place - the way you put it back together should be fine, but just as a reference -
My old Case backhoe has several cylinders that are about half again as big as typical toplink cylinders for Cat 1 tractors (I have 2 of those also, both with hyd toplinks) - the rod nut for the Case cylinders calls for 450 ft lbs torque (fine thread on 1-1/2" rod) and my glands have holes in the end like yours - I've snapped off 5/16" bolts loctited into 3/8" flat bar trying to get those glands off, couple I had to get close to cherry red with a rosebud before they'd move, even with a 3' pipe wrench and a cheater bar.
Granted, the ones on my hoe are bigger and have likely been in place for decades, but my point is these suckers need to be TIGHT - and again, it sounds like you're good to go as you did it; the ONLY time that rod nut should come off is AFTER the rest of the cylinder is dis-assembled, and after spending the last 35 years of my working life in heavy industrial maintenance I would NEVER trust a NyLock nut in that environment (running in oil) WITHOUT doing what you did with thread locker. Good job... Steve