Well you should be able to do it with custom SQL as long as you get the syntax appropriate for your database.
What database are you using? Presumably one that doesn't support FULL OUTER JOIN directly or you could just do that in the Custom SQL. If it doesn't support it directly, the syntax you need for emulating it depends on your database. Have you tried Googling for [your D/B] and "full outer join"?
I'm trying to connect to two large MS Excel sheets. My initial goal was to implement a FULL OUTER JOIN, but settled for a simple UNION ALL, as described here: http://www.tableausoftware.com/support/knowledge-base/custom-sql-join
Not sure how I missed that KB article at first...but this worked for my needs.
Thanks for being willing to help!