Jan,
Have a look at docx4j, this allows for merging word docx documents. See this site for example
I do this almost daily. I use a PDF merger driver found on the internet . Install it and it becomes a selectable merger option.Then you can merge PDFs into one in any program at all, including Adobe Acrobat . Just open the PDFs, select merge, and choice the form you want, the task will be finished in several seconds. if you haven't found a good choice , you can have a try. best wishes.