>I upgraded to latest version and have a link on click popup window (full controls), but when i save it to the home screen it is opening the pdf in a new window without back button or toolbar. Any solution for this?
No, this is how webclips/homescreen webapps function on iOS/mobile safari created by Apple. Mobile safari hides the addressbar and button bar. The only option I know of is to create a native iOS app that you can open the PDF file using the GotoURL popup window option.