If the counterweight is rubbing against the spacer it could be that the flexplate is warped or there is too much endplay in the crankshaft. This could be caused by a worn thrust bearing or, since the engine was rebuilt, the crankshaft thrust surface is worn excessively. Another crankshaft will need to be installed. The thrust bearing is part of the middle main bearing. This would be an issue caused by the engine rebuilder not checking the crankshaft endplay spec. before completing the rebuild.
The transmission has to be removed to access the torque converter and flexplate or the engine with the
trans attached will have to be pulled. I have found it easier to pull the whole thing, eng and
trans at the same time. With the problem that you have, if it's not a warped flexplate, the engine will have to be removed to repair the excessive crank endplay.
The only other reason that the counterweight would make contact would be that the weight wasn't attached properly by the manufacturer. I wouldn't try grinding any material off of the weight to create clearance as this may cause an engine vibration.