When I tore down the motor in -G-rim I found the same surprise like you...my balance shaft belt was torn and it looked it was like that for some time and luckily it didn't destroy the Tbelt.
Basically you are running a motor with the balance shafts eliminated in a way. You should be ok running like that, but its good to fix it when you can. The mark to where the oil pump pulley should be inline with the crank is for balance shaft sycronization purposes..if anything you should of noticed a little bit of vibration from your motor since the Bshafts aren't rotating and counter balancing each other. VFAQ will have the shop manual how to line it up or your Chiltons.
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