Then I need educated on installing pinion nut. I have a torque wrench but am unfamiliar on this special tool you guys speak of. The pinion gears do have very slight rub marks on the tip. So it does look like the pinion slipped away from the yoke and made contact with the internals. Ill do some research but would appreciate any feedback on how to make sure I'm I'm doing this right the first time. Really don't want to take to a gear shop but will if I need to.
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I don't see any REAL damage to the pinion gear teeth. With the forces related to the gears getting the marks you have doesn't surprise me. The ARB in my CRD60 is marred up worse than yours. But I also ate some teeth in mine. IMO if it was mine I'd run those gears just pay attention to any noises and don't ignore them.
As already stated I'd get the FSM and following the book on how to replace a seal. If you don't have the inch lb torque wrench you can rent one from a parts store many times.