I think I would concentrate on why the PDFs for the PPT and Excel are not A4. Resolve that issue and you should be set. I do not think it is a merge issue, unless the merge process is doing the conversion at the same time. In that case, check the properties of PDF Maker in each application with the corresponding file.
I had this same problem. I sent someone an 8 page document to which they signed 2 and scanned and returned them. When I tried to replace those 2 pages into my original (giving me a complete and signed document) the pages I inserted were smaller than those of the original.
DO THIS: Mouse over the bottom left side of the page in Adobe Acrobat. You will see which pages are WRONG. In my case, it was the originals that were too large. I then printed them via Adobe PDF Printer. Select "fit to printable area" (checking those dimensions to be at 8.5x11) When the document was printed this way, it was easy to fit those other pages in as they were all now the same size. No messing with the zoom which is a nightmare.