Maybe some gears look a tad sharp, but I think that's just the angle. I think it could very well be a possibility that your phase (in the ESC, not necessarily the motor, though the motor phase going kaput is a possibility) is blown or something is not right with the ESC if the diffs are all well and good. Did you install those purdy diff housings yet? Maybe there was a little slop in the stock gear case, and the aluminum bits will help align things nicely (and thus prevent any clicking).

I'm more inclined to believe it's the ESC, just from the videos. Especially as you say, it runs fine if you pick up the truck (very little load), but stutters like mad and does that odd twitchy crawl on the ground (not a ton of load, but an appreciable amount compared to freewheeling in the air).

I dunno dude! I say trouble shoot the electronics next if you or anyone else can't see any issues with the gears.