I'm so sorry this cake was such a pain for you. I hate it when cakes fight back
Let's see if we can troubleshoot a few of the issuse in hopes you won't have this much frustration next time.
How long did you let the bottle dry? It takes a while. I dried my gumpaste on the bottle for 2 days, then I removed it from the bottle and flipped it over so the inside could dry for another day. So it took at least 3 days for the bottle to dry.
For the vodka corn syrup, when you say blotchy was the shine blotchy or the color blotchy? I did apply a couple of coats to my bottle. I applied them back to back without any drying time between them. I'm wondering if there was any shortening on your bottle that caused the syrup/vodka mixture not to adhear to the bottle that would cause the blotchiness in the shine. Can't think of anything else that might cause that. If the color was blotchy it could be that the color wasn't mixed fully into the vodka/syrup mixture.
My panels were not straight straight either but I am learning to get past my perfectionist issues and step away from the cake and come back 15 minutes later with fresh eyes and see what I think. And if you've ever looked at a wooden crate there is nothing perfect about them. They have gaps, uneven panels and seams
So really your crate was realistic!
If you're going to do panels on cakes, I highly recommend Sugar Shack's Boxes and Bows DVD. It has an outstanding walk through on working with panels, making them even and hiding seams
What did your sister think? Was the cake a hit? I ask because my guess is you're the only one who saw the minor imprefections.