Daveg is right. The front deck strips that continued to rise up rather than curve down to the rear deck are holding the middle part of the template too high. As a result, the sides can't reach out as far as they need to.

A bit of work with a heat gun, clamps, bits of rope and anything else you can lay your hands on should be able to reduce the problem sufficiently that with a bit of imagination, you can use the template.

The cutout for the recess does not have to be exactly the shape of the template. Just as long as you get a fairly smooth curve on the outline that is similar to the cockpit itself.