Having played this game more then once I have to agree with Drew. First, track down the differences in the databases and data and figure out how to reconcile them at a buisness level. You will probably have to send some of those issues back up to your manager to setup cross department meetings to figure out how to reconcile them.

After that the technological problem is actually much simpler. Depending on how much data you need for your reports, how current they need to be, and how often they are generated, you have a bunch of options.

Jay