Doing is the fun part. And thanks, I'm glad you enjoyed the post. Something good became out of this.
I do share the pain you're going through. Something tends to always go wrong and sadly, too short parts are harder to fix than the too long ones. You can't saw away yourself any more wood :)
I'm not sure if I'm going to paint the birdhouse. I'm not sure which paint would be the safest option to make sure there are no possible health effects to the birds or the nature around it, but I do agree the design is not the best possible one. However, the merganser birdhouse is a special design, as it's supposed to be on the ground.
A large enough piece of plywood would have made it look better, but maybe next time - when I'm not using leftover materials.
And thanks :)