I am sure you are right about there being two john Moodys, one at Cullyvenny and one at Ballymoney. My John Moody is listed as a blacksmith in Ballymoney as early as 1846, and as you say, the two appear in their respective locations in Griffiths Valuation. Based on his age at death, it seems my John Moody was born circa 1803. That puts him in a timeframe that could make him the brother of Matthew of Cullyvenny. We have a number of pieces of evidence to suggest the connection between Mathew at Cullyvenny and John at Ballymoney. The fact that Matthew's Will dated Sept. 5th 1860 names John Moody blacksmith of Ballymoney as an executor of his estate is the clearest connection. It is significant that my great great grandparents, Mary Moody and David Reid Cathcart were married at Cullybackey in June 1868 by Rev. Joseph Archibald Moody. Also the witnesses to the marriage were Jane Moody, Mary's sister, and James Galloway. This James must surely have been the one who married Matthew Moody's daughter Mary in 1850. There is also the fact that John Moody of Ballymoney named one of his sons Joseph. I guess we need to compare all the references we can find for the two John Moodys.
I have just found a reference to Matthew's son, Robert John Moody, still being in Castlemaine, Victoria, Australia in 1902. Joseph Archibald Moody's Will of Jan. 8 1898 gives that place as Robert's address. It seems Robert had a son Robert who was in the New Zealand Army during the Boer War. I live just fifteen minutes from Castlemaine, so will do some checking.