Prompted by your reference to James McLoughlin, aged 64 buried in 1847 I revisited the Craigs church records. I see there is also a Betty (Elizabeth) McLoughlin, aged 70 buried in 1848, so it looks as though these may be William's ( and Robert's) father and mother - both of whom you have information on from Robert's Scottish death certificate. The name Elizabeth carried down both sides to the next generation because my GGgrandmother (William's eldest daughter, dob 1850) was also called Elizabeth.
From my reading of the church records there seems to have been only the one McLoughlin family in the CoI congregation.I know from my grandmother that they lived at Hillmount. The Robert mentioned in the Griffeth's Valuation is William's second son, with whom she lived as a child.There is a grave marking his family plot in Craig's churchyard.
I was aware there were other McLoughlins in the Presbyterian records but, until your reply, couldn't see any link to them. I will now have a more careful look through these.
I can also try to follow up on the very helpful information from Elwyn Soutter pointing to the earlier Ahoghill church records.