In which order should I prepare my PDF so that everything works ?

Question

So I have Pages document that I save as PDF via Print, then I generate sidebar bookmarks with PDFOutliner, then I want to do several things with Acrobat 9 Pro:
• allow commenting (I saw 2 ways of doing it, Comments menu and Properties > Security)
• allow print
• forbid copy of text or any other way to retrieve data from the PDF (though I’d like to let screen readers access the text -- I encountered an issue, the first time that I set securities the summary was saying all was allowed but in other softwares it was different, and in Preview  I could copy text without the PWD)
• add additonal metadata
• specify initial view
• add full text index & catalog (and perhaps also an embedded index if I learn the difference -- none worked probably because of earlier security settings)
• define advanced properties
• optimise the PDF 
There you have it, so in which order am I supposed to do all this so that there is no conflict ? 
P.S. I’m have to hand in my finished work today but I didn’t expect the PDF part to be so complicated, so I would be very thankful if you helped me in my urgency.

Answer 1

Security always goes last, the rest don't matter. Catalogs are for searching more than one document at the same time, they have no value in a single document - if the PDF file is very long you just want the "embedded index" - but the gain in search speed will only be noticeable if the document is huge. You probably won't notice the difference below 50 pages.
So you could go:
Optimize
Add an embedded index
File > Properties
add metadata, add initial view settings, extra properties, etc.
On the security tab apply password protection and choose your permission restrictions.