I can relate!
I think I also did something backwards, but not in opposite directions. I started the second clog and got interrupted by life about a month before the last step on the second clog. When I finished the 3 needle bind-off on the sole, I realized it looked different than the first clog. I double checked the instructions and suspect I did the first clog backwards but can't remember what I did.
If the sole is not going in the opposite direction (which sounds like what you described), I must've picked up the stitches on the wrong side of the upper clog. Maybe it won't matter once they're felted as long as they match, right? I don't want to redo the first clog because I've already sewn most of the center sole and woven in the ends. It was midnight and my brain muddled when I discovered this mess, so I detached the sole on the second clog and went to bed. Am hoping I can figure it out today.
Did you ever get your clogs out of the closet and finish them?