You shouldn't need to do any re-wiring for a 6 pole plug. Just use a 7 pole to 6 pole adapter like this one...

Adapter

You should be able to find one that will work for you at any auto parts store.

I have a Tekonsha Prodigy brake controller that works great, doesn't need to be leveled and is easy to wire to the 4 Runners factory plug in the left side kick panel. You will need the wiring pig-tail from Toyota to make the process very simple, my truck came with one.

Tekonsha Prodigy

I'll post some pictures shortly.

Watch the video on this page...

Video2

They install a brake controller on a 4th Gen 4 Runner. You will see how easy it is.