I'm about to start this same project. My situation is a little different. My 4runner is a 1990 and originally had a swing gate. It was rear-ended and the old tailgate was replaced. The PO kept the swing gate, the old tailgate and all the bits and pieces. So, fortunately I already have the correct rear quarter panel and all the parts, I just need to retrofit the new tailgate.
Diverse4runner and willyt4r, have either of you made any progress? If I get to it before you all, would you like me to post some pictures here?