For filling the holes you could back it up with fiberglass and bondo over the top. Evercoat makes stuff called Tigerhair that is a ***** to work with but is tough. It has chopped fiberglass in it. As far as removing the latch for the trunk, why not use either hood type pins or fasten it back down using Dzus 1/4 turn fasteners. The dzus fasteners are what you see a lot of racers using to hold panels on. They are spring loaded and only take a 1/4 turn of the screwdriver to release them.
Kevin
Kevin