I have used jb in places it was never intended for with fair results, kind of rough up the spots for jb so it has something to grip to. good luck.
I was told small dings are generally fine, as long as there are no sharp bits that may cut the seal. If there are bumps coming from the rod, you can rub them down with an oil stone.
New bobcat rods are case hardened, not sure about the older ones. If the cylinder rod has dings as you say, i'd suspect it's not hardened. The hardened ones take a LOT to mark the outside.
Depending on how bad the bend is and how much wear the gland has, you may get away with a set of seals.
If you can pull them apart and get them to a hydraulic seal shop, get some pre-energized pressure seals. I don't know if yours have these already, but they do an excellent job of holding back any drips. I had a tilt cylinder that used to drip, two seals later it still did it. They gave me a different style seal, not a drop since.
Bobcat use this style of seal now in newer cylinders, again, not sure about the older ones.
This style of seal is a little harder to install as it's thicker as it has an energizing ring, but worth the extra fighting that you do to get it into place.