1. It will take usually between 3-4 months for a vehicle to go from beginning of assembly to your dealership lot.
2. You cannot "special order" anything. For example, you can't get a green interior in a purple 4Runner. If it exists on the Toyota website then you can get it.
3. Your dealer usually orders many months in advance based on what he thinks he will sell. Every dealer is different though and what one likes the other doesn't. Dealers can sometimes "trade" inventory and that could get you what you want quicker.
4. Toyota is different from other vehicle OEM's in the fact that the dealers do not buy directly from Toyota proper. Toyota has distributors scattered around the country that dealers order from. Some of those distributors choose not to order some options. Example: A Trail Edition with KDSS in Florida. They will sell many more 2WD units and the 4X4 units could sit on the lot for a long time. When you order something unusual from the dealer, he orders it from the distributor and they in turn order it from the factory.
5. Many options, such as floor mats, roof rack cross bars, running boards and remote starters come from the distributor. These are called "Port Installed Options" and they are OEM Toyota components.
So, to summarize, you can get something in 3-4 months, quicker if the dealer can do a swap with another dealer and if you live in certain parts of the US you might not be able to get what you want from your local dealer because of the distributor and if you want something other than what's on the Toyota website you cannot ever get it. Got it?