This may not be final since the hinges might allow some movement.
With a belt sander I marked and sanded, marked and sanded until I had an even gap of about 3/32" all around. It is not perfect because there are some irregularities in the cabin top that will need a little attention.
I did not have to move the alignment holes at all. With sanding, the door slowly transitioned into the hole and a flush fit. Beveling back the underside of the door to fit the curvature of the canopy gave about 1/16" clearance.
With the door fitting slowly into place, I was finally able to sand to fit the canopy opening edge. A 4 1/2" angle grinder with a medium flap disk makes quick work of the final shaping.