 <p>FYI for anyone else that stumbles on this:</p> <p>We ended up taking a different direction. It seems that iPad/Safari get to choose what happens to your PDF. We ended up taking the route of minimizing links in PDFs instead. The closest we got to an actual solution was hacks that some PDF readers use to change the protocol: eg ghttp:// for url that opens in GoodReader. Did not find this to be an acceptable approach.</p>