I think a hot glue gun would be a non-starter, it would be far too hot for the job.
I always use beeswax, with a small percentage of resin melted into it. That's what the pros used to use. I don't know if something better has come along, but they used to frown on candle wax. ( I don't know what the problem was, but I followed the advice ).
If you heat the mix that I use too high, it goes black and looks ugly. I have a controllable solder iron that I use, I can adjust the temp to the minimum that will do the job. If you don't disturb the wax too much when you remove the item, you can usually reseal it with minimum extra waxing.
I still suspect that you'll find that when you get the wooden plates off, they will fit ok when turned around, and line up without too much trouble.
It's more likely that they were fitted wrong, than actually manufactured wrong.