I stained the first part on Sunday and it was darker than I wanted, but it was tolerable
I spent Monday trying to figure out what to do next. I really don't like painting wood, even plywood. I tried sanding down one of the sections of plywood and the stain came off fairly well, so I decided to give it a shot. I started out by stripping the boards. I tried to sand them in place, but it really wasn't going to work because I couldn't get to the edges, so Jeff uninstalled them for me.
I already bought the proper stain and I took it to Sherwin Williams and had it shaken. I will not be making this mistake again. Ever!
Now that all the boards are removed, I am going to go ahead and stain them loose like I usually do. It should also make it easier to stain the wainscoting. Once everything is stained I'll reinstall the boards and then apply the varnish finish coat.