I just use some random grease I have lying around in the diffs and the gearbox, out of my Dads garage, haven't got a clue what it is!
With regards to your spur and pinion, I was told ages ago to get a thin strip of A4 paper and run it between the pinion and spur, you should be able to get it through without being too tight. If it rips it its too tight!
I wouldn't bother sealing the axles, maybe just use waterproof grease? If your worried about the damage on the ring gear then replace them. I've never had any bother with my SCX ones but I rounded a pair off in my wraith, but that was brushless. If they seem to mesh ok and don't slip they should be ok.
Steven