I'm looking at 16" TRD wheels (6 x 5.50 or 6 x 139.7)

http://www.ebay.com/itm/Toyota-FJ-Cruiser-2007-2014-TRD-16-BLACK-Alloy-Rims-Set-OEM-NEW-/131109767685?pt=Motors_Car_Truck_Wheels&hash=item1e86c04a05&vxp=mtr
I'm pretty sure they will work but eBay's "compatibility tool" says that they aren't compatible so I just wanted to double check with you all!

Yes and no. I have a set of txpro wheels I'm currently working on top for my 89. The problem is the hub opening on the wheels is not large enough to clear the manual hubs. So you have to machine the inner lip off the hub on the wheel a little bit to allow them to clear. Then you can't run the center caps as the lip on the hub of the wheel they snap over is now gone so the wheels can fit. That being said you can probably create another way for the center caps to go on.
But no they are not a simple bolt on and go

They will fit. Should look great. Rerunn is right about the caps. But just machine two of them, and install the caps on the rear ones.

Any more pics of your hood?

That's my plan!!! Haha
But rotating will SUCK!! Gonna have to break the tires down and physically swap from wheel to wheel but hey the price you pay for awesomeness lol