Hi Matt, to see where the holes are, set up a shortcut key with the script shown here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=6051.2

That will highlight any "naked edges" of the model - those are edges that only belong to one surface instead of being joined between 2 surfaces, those are the spots where there are holes in the model preventing it from being watertight.

- Michael