I would suggest finishing your taxes as quickly as possible. Whatever penalties and interest are due at least stop accruing as soon as you file. Figuring the number of days late on taxes not withheld by an employer is very difficult since technically you owed those taxes with each pay period from the beginning of the year. Pay the taxes now and when Pennsylvania sends a letter requesting penalties or interest you'll be able to see what they calculated and decide whether you want to pay it or argue.
@Josh C
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