Mock this thing up on you block and see if the intake lines up with the ports. From the placement of your gasket in the last picture it appears the intake will line up correctly with the ports. If so, you can probably fix this by plugging the original holes with bolts, cut them off flush, then re-drill new holes in the correct location. it looks like they will overlap the original holes a little, locking in the cut off bolts. like old school pinning technique. That should save the work you have into them already.