Re: How can you normalize page size (width, height, etc.) as best as possible while still retaining bookmarks, after combining multiple PDFs?

You would need to use a third party plug-in tool to do page imposition.  I have placed a couple of vendor links below but I would suggest you do your own investigation to find what appropriately meets your needs.

http://www.quite.com/imposing/features.htm

https://www.evermap.com/autopage.asp