I'm going to throw out my experience and how I have went about setting it up after running into some issues after a server move.
I went from a php5/mysql5 server to a php4/mysql4 box and had several issues. I could get PAN working straight up, but not integrated no matter what combination of compatibility mode settings and other things.
So, I got it back to working by itself, dumped the db, then imported the tables into my vbulletin db, changed the config to reflect the db change, imported the product again, and it works fine just like before.
The only difference is my vb db is a bit bigger, but in the end it's probably simpler than having 2 separate db's to take care of.
One other note for Linux newbies (which I was not long ago): setting the local path to PAN, mine ended up being /abc/def/username/www/phpadsnew with no trailing slash. I have no access to /abc/def/ but it still needs to be included because that's the true path to the folder on the local machine.
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