Before you go flushing the hydraulics, I would get an oil sample submitted. You can get oil samples done at your local cat dealer (I am sure there are other places, some of the more experienced guys here could probably tell you but that is the only place I personally know of). With it having been sitting it wouldn't be a bad idea to go ahead and pull samples from all compartments.
Biodegradable oil I don't have any experience with but I'm willing to bet someone here does.
Repacking cylinders can vary from simple to arduous. Smaller cylinders with bolt on or spanner heads can be done in house where larger "nut" style heads on cylinders require a cylinder bench or huge vise and pipe wrench and a crane.