Wow, I like the idea of using relatively inexpensive LED "rock-lights" on the roof rack for the rear and sides. :AK47:
The smaller 6" rigid lights I have seen installed on the sides and rear of 5th gen truck racks are pretty expensive. They have been cost prohibitive for me and I was thinking they would be a theft target. Here is a link to a thread in the 5th gen area I started that has a couple pictures of them installed.
http://www.toyota-4runner.org/5th-gen-t4rs/127991-what-light-mount.html
A couple guys have installed LED light strips that look very bright. Probably not a lot of throw, but I am thinking they may be pretty good for sides of rack for camp setup etc. Here is a link to a page a bookmarked the first time I saw them.
5K WHITE 3 CHIP STRIP LIGHT STRIPLIGHTS Looks sold out now....
Also, regarding the roof rack. I think your idea to move the rack forward of the moon roof is a good idea. More functional and aesthetically pleasing. However, I think you should consider adding a fairing to the front rather than just having it open with lights there. The wind noise without a fairing may be substantial. Look at the my pics in the link in my signature to see the baja flat rack.
And on third thought... ; ) Something like this Hella light might be a good intermediate choice. They are ~$75 each, which is a lot more than the original 10 pod set, but a whole lot less than the rigid lights I have seen ppl install. These come in white or amber and have way too many flash capabilities. I have not looked too closely, but I imagine the light output would be good for backup and side spill.
Hella HD :: MS6 & MS3 Mini LED Lightheads