Matt, I'm going to revive this thread to ask for some additional DIY info. Hope you're around to help!
First, I'm guessing that the larger magnets you've used are the epoxy-coated 3/4 x 1/8 neodymium N42 discs shown here?
K&J Magnetics - Products
What's the thickness of the glass on the tank that you're showing in the pictures? (I'm trying to determine the pull strength that you're getting after separation.)
Here's a nice page that gives you some magnet calculations (such as pull strength). I've found it helpful and thought maybe other's might, too.
Calculation Tool-Kit