Honda rancher differential rebuild?

The actual question that for some reason I've never pay attention to before is the rear differential bearings, both roller and needle in my case, do I need to grease them or will the gear oil keep them lubed. These aren't sealed bearings so I half way want to but I'm not sure I should. I would have just looked at the old ones to see if they had grease but the were caked with mud and water.

If the differential uses oil I wouldn't pack the bearings full of grease. It is not uncommon to use a bit of assembly grease to insure complete lubrication on startup. A light coating wouldn't hurt so the oil can pass through. The issue is that when filling the case, oil can't pass through the bearing so it will not fill the entire cavity. After it has been run a bit the oil will then pass through and the level will be low. This all depends on the case and how the bearings are situated in it.

No need for grease.

"but the were caked with mud and water."
water is not good. You need fluid change As soon as possible. Water in gear fluid will destroy bearings. Guessing the truck has been through relatively deep water and the diff does not have raised case vents. You should have it inspected/serviced by a pro shop you trust. And see about installing raised case vents if the need to tread deep water persists.