hi Isaac...
There is a reason for the cockpit assembly that I listed in the instructions.
In the model's building instructions, it is first necessary to insert the cockpit into the part and only then to connect the parts, for the reason that the cockpit is a little bit wider than the top opening of the cockpit.
with your method, when you inserted the cockpit from above, and because the cockpit is wider than the opening into which it fits, you have created some tears/ruptures and deformation at the top of the cockpit opening....I hope the canopy will cover that.
best regards
YOAV