No problems here but maybe you should get the dealer to throw in an extended warranty, the rear axle leaking could be a freak thing and a 1 time only problem, these vehicles are mass produced and a faulty part found it's way into 1, I've seen weird problems on certain cars enough times that I would not be to concerned about it, once they fix it, the rear end will practically be replaced/rebuilt, just be glad it happened within warranty time, they say it will either go bad or not, if it was a common problem their would be more then just you posting about it.
It's still a pain in the butt, but if you where to call Toyota and complain Im sure they would do something for you, they are into the whole customer satisfaction thing and you traded in a 4Runner for a 4Runner, they also like happy repeat buyers.
Make sure they replace your rear pads, the pads and oil don't mix, as for 1 time weird problems their was an owner who had to have 1 side (2 shocks, front and rear) of his X-Reas replaced cause a tiny O-ring was bad and oil was leaking out, considering that the X-Reas is made by Yamaha you would think it would never break
As for your trans, what are the conditions that it takes so long to shift, is it cold and does it sit, I would say mine takes 2-4 seconds but I always kinda let it roll forward before I touch the gas, mine is no rocket after I shift, their is a pause before it does shift and if I do hit the gas it gives me whip lash when it does go forward, it could also be the delayed drive by wire and the computer that learns your driving technique, if more then 1 driver it messes it up or just confuses it.