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An S corporation is required to pay its employee-shareholders "reasonable compensation" for their services so I would not back out all of your salary. You do not necessarily have to pay more in wages, but rather increase your withholding on your salary that you do pay so you get credit retroactively to the beginning of the year.
The estimated tax penalty is currently about 3-3.5% and the combined FICA and Social Security taxes are 15.3% (half paid by the corporation and deductible by the corporation and the other withheld on your wages) up to $118,500 in earned income. Once you are over that threshold, you only have a 2.9% Medicare tax that is also split in half between the employer and employee. Based upon these rates, it might make sense to just pay the penalty, however, however if you report less earned income you will qualify for less Social Security, though Social Security is not really a sound investment.
The ultimate choice is up to you and what you think is best for yourself.