Hey Cylinder heads guys- advice needed

That's a significant difference and should have been handled from the perspective of the valve job. I too would have to ask how the machinist let that go. "I guess" you could remove all the valves and cut the stems all the same....but that's not the correct way. Or, you COULD sink the intake valves to match. I cringed when I typed that. lol The most correct way at this point is to replace the exhaust seats. Contact Mike at B3 and see what he recommends. He might have some better ideas. At least about the geometry for sure. I don't see any other way to get the stem heights right......you could cut them like I said, but that's just "not right", IMO.