i know you abandoned at this point, but would there have been anything preventing TJ hard uppers from fitting on YJ lowers once you addressed this pin issue? Is the pin off longitudinally, laterally, or in both directions?
I abandoned modifying the rear most pin on the TJ soft uppers but I did actually fit my TJ hard uppers to the YJ hard lowers at one point. I had to drill a hole through the uppers so I could insert a 3/8" pin down through them and into the YJ lowers. It worked fine. I later filled the holes I drilled with epoxy and then painted the complete uppers. I use them now on my TJ lowers and the holes I drilled can't be seen.