Snowman9000,
You should be able to adjust the top lockset latch by simply bending it slightly. If you think you are adding too much stress on the door, then unscrew it and bend it off the rig.
Your door system is extremely common in the RV industry. You'd have to spend really big money on a high-end rig to get a better door system. Most of us are in your boat, me included. Fortunately I have not yet had any such trouble. I did adjust my latches so my two sealed/gasketed doors require a bit of a push at the lock with my other hand while turning the key to assure the gasket makes good contact.
You got the right idea on drilling two new pin-holes at the bottom. But I would leave the side drain holes alone, allowing the inside of the door to breathe. If that is later determined a bad idea, then dab them with a little silicone caulk which is easy enough to do anytime, even during a trip.