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Ah, right you are! I was so confused before. I followed what you said here, and it went together just fine.
I have another suggestion. At first, I printed out all the pins full-scale and spent a lot of time sanding them, re-fitting them, etc. It also occurred to me to use the drill trick you mentioned. Occasionally I'd over-sand, and instead of printing a new pin, I'd heat it up with a hot air gun and use some pliers to push the two halves of the pin apart, making them fatter.
BUT - I eventually settled on a much simpler solution. I loaded the pin into my slicer three times. I set one to 95% scale, another to 90%, and the last to 85%, then printed them out. I discovered the best fit was somewhere between 90% and 95%, then narrowed it down to 93%. At that scale, the pins fit just about perfectly, without any sanding. Then, I ran off another 6 copies of the pin, then did the main cube pin and some others, also at 93%. I would like it if these pins kept the original 100% of LENGTH, but what they've lost in length doesn't seem to be enough to stop them from holding everything together.
I would say that if you work on a new version, an assembly video, or even just photos of the parts where orientation is easy to get wrong, would help a lot.