re: copy from MoI to Illustrator - using either AI format or PDF format should work but you'll probably want to use AI format since Illustrator does not read layers from PDF files.

According to Adobe, Acrobat is the main thing to use for editing PDF files and it reads all sorts of PDF specific stuff that Illustrator won't really deal with (see Adobe discussion thread: http://forums.adobe.com/thread/509192).

But possibly for other illustration programs or other more PDF specific programs like Acrobat using PDF on the clipboard would be good.

- Michael