Yeah, I see your point, your 4runner's raised bars starts at the "B" pillars, would be nice if they gave you another six inches up front.
What you need is an attachment for another bar up front. Turns out it isn't so bad. Here is how I would do it.
http://thule.com/en/US/Products/Bas...irect Mount TK Base for Sheet Metal Roof.aspx
We used to call these "landing pads", they look like little nubs on the roof when you take the bars off. The trick to these is to get good placement. You want to mount them right into the roll cage of the truck. I like to set them up wide, almost at the edge of the roof, where it turns.
So, I would set up one Thule bar forward on "landing pads" and have two crossbars back on the raised factory bars, I like the old low profile Thule 440's. The tricky part is that since you will have three bars, they might not line up on an even plane. I used to "pad" the front and rear bars so that they would all line up. If things wouldn't line up quite right, I'd cut a couple strips of plastic or wood to place on top of the front and rear bars to line them up. The square "U" bolts might not be long enough to go around the now thicker bars and pads so you can replace the "U" bolts with longer 1/4 inch carriage bolts. AutoHome's mounting plates are designed to allow carriage bolts. If your bars still don't line up exact, it isn't a problem. Think of a Maggiolina or Columbus as a big fiberglass spring, they will take up 1/2 an inch easy.
It will take some fiddling to get it all set up but most shops that do custom installs of Thule stuff shouldn't have any trouble. In this case I prefer Thule's square bars over Yakima's round, they allow for easier adjustment. If you have a good shop, have your tent shipped direct to them and they should be able to get it all done in a couple hours.