Crewchief,
Your post sounds like you've thought things through pretty well and are doing a good job overall. You might still reconsider your top insulation, though. First, it sounds like it's covered your fan snap disc, which is your first line of defense for safety to remove heat. If your front temps get up to 300-350 before the fan kicks on, I think mine comes on much sooner (like 150F on the front face). You can probably heat your house even better if you get the fan running at the right plenum temperatures.
Second, I agree your temp controller should prevent over temps, but I wouldn't rely on it. There's no harm in retaining the functionality of the original snap disc. It can't hurt, it can only help, and you don't lose any heat by keeping it enabled. Also, what happens when you sell the house, or the furnace, or remove your temp controller, or who knows what in the future and some unsuspecting person, perhaps yourself, no longer has some form of overtemp protection.
In my opinion, when dealing with fire I try to design for the unexpected, not only the expected.
