Prior to removing you should have done a bypass test to see if the piston seals were leaking.
Too late for that now, seals are cheap so Id rebuild and use if it was working before. Check the rod for straightness or for nicks/scarring. IF its fine it probably only needed new gland seals
I suppose I can do this bypass test with the other cylinders. Once I know how.
Could be only the gland seals were bad, but, no point in going that deep without changing all of them.
The rod is not scored or nicked at all. There are some "polished" areas. I don't have any v-blocks, but can probably find a way to check straight.