My son sold his home in December 2006. In 2007 he and his wife were accepted by a mission board as missionary candidates. In 2007 and 2008 they traveled over 100,000 miles in the U.S. on deputation presenting their vision in more than 100 churches to raise support to allow them to go overseas. Finally, he was commissioned by his home church to go overseas as missionary in March 2009. They are now on the mission field as missionaries. In 2007 and 2008, he paid SECA tax; he did not claim a housing allowance because he had not been commissioned and because he was moving from place to place. Occupation listed on his tax returns was "Missionary."
Having paid SECA in 2007 and 2008, has he missed the two year window to file form 4361 due to a conscientious objection over religious beliefs? Or can he now file and consider the self-employment income (1099-Misc from Mission Board) as marketing income since he was not on the field and was not commissioned yet by his local church?