Bell-housing alignment help

It was align bored or honed, not sure which of the two, but the bell definitely needs to go down. I've put the offset dowels in, and I know which half of the bell mounting bolt holes I had to enlarge on.

I don't see how it would even be physically possible to displace the crank down, barring some lunacy involving eccentric or oversized main bearings, or adding shims. So from there, the only other option involving the engine half of the equation is... if the alignment pin holes were machined in the wrong place on the block, back when it was first built?

Per suggestions above, I'll check the face and edge of the crank vs the block, and I'll check the face of the bell vs the crank, see if they're in the same plane or cocked up. This weekend, maybe, if I can get away.