Not all related to the 4runner, but do these things:
1. Purchase the book, "Water Dog", even if you don't intend to hunt with the dog. This guy is spot on in so many ways.
Water Dog Book on Amazon
2. Definitely crate the dog at first. Also, don't pay full price for the crate(s). People sell them on Craigslist all the time, and they don't command nearly as much money as they do new. So, generally people are practically giving these things away.
3. It's always a good idea to crate your animal while driving on the highway, etc., but I don't do it. Instead, we flip forward the 60% rear seat, and put his padded bedding there, without putting down the seatbacks. Works pretty good, and in theory, would keep him from flying through the middle of the front seats in a head-on collision.
4. In the rear cargo area for short rides to the dog park, etc., my Husky liners have been perfect, but if you have a Lab, I would also use the Canvas covers. He can get back in there totally dripping wet and it's fine.
5. Bear in mind that he can jump out of the back window! Mine did once when he was a pup. Scared the sh!t out of me! Also, the exhaust pipe should be bent to the side to reduce the amount of exhaust coming right into his nose when he's hanging his head out of there...
Hope that might help...