Yep, they will work. I just installed the off-road y-pipe form URD. They are actually a much better fit than the stock pipe which is very restricted. URD has re-routed the pipe section that goes underneath the transfer case so that it doesn't get pinched and sits closer to the frame.
I have the pipe that is for the 2008 Tacoma 4wd. The only mod to the runner is the hanger on the y-pipe is on the drivers side where as the hanger on the runner is on the passenger side. You just have to relocate the hanger. Additionally, where the end of the y-pipe attaches to the cat back section, there will be a 6 inch overlap because the y-pipe extends further back than the 4 runner pipe. So you will have to cut and shorten the pipe that goes from the connection to the muffler. Other than that, it fits perfectly. I hope this answers your questions.