Sorry for the delay in responding; I had appointments away from my office today.
This how the due date of the 4361 is expressed by the IRS instructions to form 4361:
"When to file. File Form 4361 by the due date,
including extensions, of your tax return for the
second tax year in which you had at least $400
of net earnings from self-employment, any of
which came from ministerial services."
That would appear to be the due date for the 2015 return, including extensions, which was 10/17/2016 if you filed for an automatic extension to file Form 1040 for 2015.
However, the granting of a Housing allowance in February 2014 isn't relevant to the timely filing issue. As you can see from the instructions to Form 4361, the key is the year you received earnings as a minister. Even if that was 2014, the timely filing requirement has expired.
So, if you are to continue to seek exemption from Social Security Taxes; the only potential viable alternative is to respond to the IRS's request for additional information. Starting over, doesn't appear to be an realistic option.
As an aside, I feel compelled to ask whether or not you have considered all of the ramifications of being excluded from Social Security coverage. One of the most significant benefits of being covered under Social Security, is the disability coverage should any unexpected accident or illness cause you to be unable to perform your normal duties as a minister. Also, the retirement benefit is substantial and should factor into your decision to seek exemption from Social Security; these benefits extend to your family members also if qualified to seek benefits under you earnings record. As a retired CPA, I can tell you that without the retirement benefits from Social Security, I would have a difficult time maintaining my current lifestyle. In addition, if you are married for at least 10 years, even if you were to be divorced, your ex-wife(s) would be eligible for benefits under your earnings record.