Nima, I didn't post all that before becuase it's a lot of data for people to wade through and I don't think it will make any difference; since I can take a slow query, say the one from /dotlrn/admin/users that lists the users of a particular type, and get just as long a run time running it from sqlplus as I get through the browser, I believe the root of the problem lies at the system/database level, not in the application. However, since we want to get to the bottom of this I'll put together a list of what you've asked for.
In particular we do not currently have PermissionCacheP turned on, but in that thread you reported having some trouble with it. Since this is a production system I don't want to turn it on if users might encounter errors. Is it is working cleanly now?