It's not possible to merge PDF files with Reader.
I'm not expecting Reader to do the merging. The merge would be done with an application, or a script on the CD itself, which would then be saved to the user's desktop where they could view it with Reader, which is the only software I can be certain that the user would have on their machine. Possibly the CD could contain an application that would install on the user's computer, which would do the merging, but we can't expect the user of the CD to have to buy an application to use it.
I don't think that's possible.
I'm pretty sure it is possible, but doing it from scratch requires a level of programming beyond me. We actually have a version of this, working on a .asp web page, but I can't find a way to make it work on a stand alone CD. (the page is not visible to the web, internal only)
Sounds impossible to merge PDF together with Adobe Reader or if the files are still HTML format. Of course, if your file type is PDF, you can easily combine many PDF files into one using PDF Merger, Acrobat is not needed. And hope that helps.
I see no problem only some work to realize it.
For merging I would use a freeware command line tool like pdftk or mbtPdfasm.
You should have a look at: http://www.becyhome.de/download_eng.htm#becypdfasm
That's a nice GUI for mbtPdfAsm and - more important - the only freeware tool which supports predefined/changeable batch-jobs.
So maybe you can avoid to write some JS/VBS/HTML/HTA code.
In general I would prefer a "own GUI" so you don't depend on some System-settings.