Yakima claims to have a rack for virtually every situation. Go to their website, get their phone number and talk to a rep. That will answer your question as to whether you can get a rack to fit your factory rails. If they don't have it, I really doubt you will find it. You may be stuck with towers that clip to your roof at the door opening and forgetting about the factory rails.

85 4Runner 22re, mostly stock. Over 340K miles(SOLD for $4000 7/06)

98 2.7 4cyl 4Runner Bone Stock perfect 200,000 miles (alright, it has a HG and clutch in it's past)