Convert uploaded files to pdf and stamp

I have a website that currently allows users to upload files through RAD Upload software. ([login to view URL]) I think the current process is good, and RAD Upload should not be removed, but I need to have these files converted to pdf when uploaded and stamp the top and bottom of each pdf page with the website name. Most files uploaded are text files. (.doc, .html, .txt, etc.). Some are uploaded as pdf already. Converted files must all be searchable after they are stamped by using the pdf search feature). Also, I am interested in changing the file link throughout the website. The current link: example: javascript:__doPostBack('rptFiles$ctl00$lkbViewFile',") does not allow search engines to locate the files. I'd prefer if there was a change to this link type, or an additional link added to each page so that it could be viewed easily by the crawlers. Site link is attached.