If you were an independent contractor and you received this amount, you need to include this in income whether or not you have a Form 1099 Misc. Church can correct and issue you a correct Form 1099.
Since this is self employment income you report this on Sch C, You can take deductions for necessary and ordinary expenses incurred by you while carrying out these services.
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Please note: This advice is provided with the understanding that all the relevant facts have been provided by you. Any change in facts might affect the advice given and hence may not be relied on in such cases.
Since this is noted non-employee compensation, it will be reported on Sch C. You can claim the credits for education expense.