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OK, well the gearcase was assembled before you pulled it apart, so something got changed while you had it apart. Any new internal pieces/gears? How about removing the prop shaft and gears, then trying to assemble the two halves…. If the halves go together OK with no internals, then there is some issue with parts you have replaced or how you have installed the original parts. Are you sure no parts got accidentally mixed up with another engine/project? Do you have the gearcase off, or are you trying to do this with the upper gearcase housing still bolted to the exhaust housing? If so, I would probably remove it and secure the upper gearcase housing in a suitable fixture where it can be flipped upside down. You mentioned the bushing locating pin being pressed into the housing, are you sure that bronze bushing is seated properly into the housing?