Toyota makes a handful of "standard" builds for each model in each region of the country. For example, in the Midwest, there are currently 4 such configurations for the V6 Limited, and 6 configurations for the V8 Limited. So, it's true that you can't hand-pick your own set of options and necessarily expect to find a car that way on the lot. These standard builds are what you'll find in stock on dealer lots or being delivered in the next few weeks. Of course, you can special order anything from the factory, but you're looking at waiting about 4 months.
You can find out what the standard builds are in your area by doing the "Build and Price Your 4Runner" thing on Toyota's Web site. Go to the 4Runner area, and then you'll see the menu bar along the left side. It will ask for your ZIP code - that tells the system which region you're in.
As for colors, that's pretty much luck of the draw. Getting the color you want with the option package you want might be tricky, or it might be real easy. Any Toyota dealer can tell you what's available and what's coming off the boat at the port in the next 3-4 weeks.