Yes, definitely proper bolts for the doors - not sure what sort of wildlife you are dealing with but certainly in the UK a fox/cat/dog can easily open those little wooden twists.
Clear tarp or a shower curtain makes a good rain cover
It's more common to keep outdoor bunnies in the UK than US if you need any ideas. If you know anyone handy with DIY it's very easy to extend them by adding more run space at the bottom - water out for digging though!