The guy I know cut thin timber (around 1/4" - 3/8" thick x 1"- 1.5" wide) timber strips the length of each of the three sides of the cut out. He cut matching pieces for underneath the roof.
He put one piece on top, one piece underneath and G clamped the two pieces together, crushing the seal down evenly.
Repeat on all seal surfaces....leave in place for a couple of weeks.

Wish I had the pics to show you.....he did it on a Fisher roof, but it should also work for Hurst Hatches.....his tops fit perfectly after he was done.

Thanks for the detail mate.

I'm not as handy as most people.

Your descriptions good though.  I can see how it would work.

Only one thing to do, that's give it a shot.

Appreciate your help.

Let us know how you go.