I have a copy of the files and database, but setting it up is not that
simple. This vb.net is licensed and we don't have license for.
If I could profile the app I'd be more than happy, but that's not going to
happen anytime soon.
What does the vb.net stuff do? Is it the frontend (eg for data-entry) or is it used on the server-side of things?
Can you profile the php app separate to the vb.net stuff?
First step is usually the database.
Get adodb (either hack it or see if it has an on/off setting for this) to log all of your db queries and see if any are missing indexes or need attention.
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Postgresql & php tutorials
http://www.designmagick.com/