Hi, new to this site. I am doing the same install on an 07 single cab. I thought the same thing about the engine bay/cabin harness. It seems as if the plugs won't fit or are the wrong type for the plug on the relay harness, which you buy separately if not previously installed.
I actually went back to toyota to complain that they had sold me the wrong harness only to look like a dumbass when they explained that you have to take off the covers/blanking plugs on the relay harness. Actually, they didn't have a clue what I was on about and told me they had sold millions of these and I was the first one to have a problem with the harness. I guess they are just there to protect the connecting pins whilst the plugs are dangling around in the engine bay - not connected. And to protect the left-over plug from damage if you don't end up installing a bull-bar.
TIP - If you take a very close look at the plugs on the relay wiring loom there is a clip to release the blanking plugs. This is mentioned in the manual.
I bought a toyota tow bar recently from the wreckers, it was in reasonable condition but being from a mining vehicle - was covered in red dust and some rust. The hitch was completely stuck, which the chap didn't mention when I bought it, so I heated up and whacked it out with a sledge hammer. Then I took it to get sandblasted and powder coated and it turned out a treat. Installed it on the back of the ute already.
In the process of installing everything as we speak and was trolling the web to see if I could get any tips for the installation. And so that is why you are listening to me yammering on.
Will post some pictures as I go through the install if anyone is interested. Although I don't really know how yet.