magento update and point code at new data base

Update magento from 1.3 to latest stable version (1.4.1.1) remove the "1.3" from urls throughout site (e.g. [login to view URL] should be [login to view URL]) fix graphs getting data from old database. We have a table that is populated every night with new data (from google adwords api and screen scraper app). We have graphs that present that data within the site, but the graphs are pulling data from the old data base and need to be pointed to the new database after the upgrade of magento. Problem Reported by internal programmer: I spent a couple hours trying to get the graphs to work again on antivisit. If I point the site to the old database the graphs work and its the current version of magento. If I point it to the database that is being updated nightly then the graphs no longer work. The two options is to point the crawler to the other database or get the developer to fix the graphs.