I would think so. The flywheel is balanced. Unless the holes were drilled PERFECTLY, removing the exact same amount of metal in each hole, it would probably be slightly out of balance. The chances of drilling all 4 holes perfectly and removing the exact same amount of metal, I would think would be slim.
Is this a different flywheel from what was originally on the motor? if so, and if you still have the original, you can take the two into a balancing shop and have them "Match Balanced". It could also be that the clutch kit is not well balanced, or as RTM posted, the holes were not drilled concentrically. Either way, I'd take the flywheel and clutch set-up in and have it checked.
BTW vibration caused by this kind of thing should be noticeable when in neutral and when the engine gets to a specific RPM. If the vibration is only noticeable when in gear and driving, it's more likely a problem with the DS or wheel balance.