Hi,
First off, awesome app. Its really refreshing to find someone who has implemented such a basic thing as merging PDFs well.
On the pagination, could you look at some customisation?
My recomendation would be:
Font
Font size
Font style (bold/italic/normal)
start position (X/Y)
Text format (ie Page X of Y/Page X/X/X of Y etc)
The interface for this may overly complicate issues, so early releases could just be XML or command line options.