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If the balance shaft is out of position it can cause a vibration but I wouldn't call it major.
If you bent all the valves as you stated did you examine the pistons for damage, and make sure that all the pistons reached the top of their travel (meaning flush with top of engine block)? I'm thinking there could be a chance of a bent rod from the impact with the valves causing this vibration.
Easy way to check it now would be to remove the spark plugs and insert a long screwdriver into each hole, put each of the pistons to the top of it's travel and see if the screw driver is the same height for all 4.
Are you sure the countershaft on the right is timed properly? This is the one with the small belt. You said it was.
Here is the way to line up the left counter shaft but the exhaust manifold has to come off. I have not found the need for this except to hold the shaft in place for gear removal. But if all else fails it is worth a shot. You already know how to do the rest of the timing so I will not clutter this post with pics. Kia knows how to make things hard.
Good luck and get back to me if necc. Wish I could feel the vibration to help you better.