@Starmanut , my pleasure!
Re: the lube, if you look like you have a ton in there already, I wouldn't bother adding much more if any. It's tough to see from here, but just use your judgement. A tiny skim of moly on the end of the male shaft might make mating them a bit easier anyway, but don't go buck nutty with it. No need I don't suspect. Now, the gears on the bevel box that mates to the gear on the wheel...that can stand a little clean up and fresh moly I bet. I did mine, and will do it every time that wheel is off.
Re your question about the shaft pulling out a bit, I suspect that it has a significant amount of travel fore and aft to accommodate the rear suspension travel. I think you're gold. Just do like I did, ease it back in there with a little lift on the rear end, and sorta "scoop" the male splined shaft up into the female receiver on the bevel box. I don't remember doing this, but I bet you could, if you can't seem to get it lined up, you could take a gloved hand and try to rotate the gear that mates with the rear wheel a little bit, which would rotate your female shaft receiver a little bit. Might just need a smidge of rotation to get lined up, but if you haven't moved anything since it was split, it should go back together just fine. Once you have it reconnected and the bolts torqued up (REMEMBER TO FOLLOW THE BOOK'S RECOMMENDATION!...it was very specific about how to torque the 4 mount bolts up in sequence. If you don't have the book, just ask here and I'll scan that page in for you), the fact that the shaft pulled out a little bit will be mitigated. It will be shoved back to the appropriate spot just by the act of reattaching the bevel box methinks.