The timing marks on the balancer shafts wont affect how the car runs. It will will great a shake or a vibration feeling when the Rpm's go up. Thats why its called a balancer shaft. It counteracts the movement of the crank to reduce vibration. It sounds like your timing wether it be cam or crank is off by a tooth. By adjusting the distributor you may have been able to get the ignition timing back to where it was before but the valve timing is probably still off.

Go back and recheck it. Make sure the cam gear marks align with the head and make sure the crank mark is aligned with the arrow on the block. I like to put the belt on the cam gear and us a clamp (like they use to hold a stack of paper together) so it doesn't fall off. Than work counter clockwise. Put it on the crank gear than the waterpump and tensioner.