Ok, if there is the possibility of your customers needing to run this on the server, you might as well abandon the idea of using Acrobat to save time later. Acrobat is only for interactive use on an end users machine. It isn't designed for heavy duty automation or mission critical work. And, most of all, it cannot be licensed for server use.
Adobe's PDF Library does then become a possibility for you to consider. Licensing is handled by DataLogics.
You can develop a certain amount of common code, using C/C++, for Acrobat plug-ins and for the PDF Library. Developing plug-ins will give you a sense of using the PDF Library.