Hey,

That is a cool tank set up you have. Yes your substrate is too deep. It should be between 1/4 inch and 1/2 inch at the most (1/2 inch is too much). I just put enough to cover the glass. This way the temperature that your thermostat is set to should be just a couple of degrees lower than the temperature on the substrate. It should help solve some of your ambient temp problems.

Cheers.