His next work was 'A Vindication of the Histories of the Old and New Testament, in answer to the Objections of . . . Bolingbroke,' pt. i., Dublin, 1752. In 1753 he published 'A Journey from Grand Cairo to Mount Sinai, and back again. In Company with some Missionaries de propaganda Fide,' &c., translated from a manuscript which had been mentioned by Edward Pococke in his 'Travels.' It included an account of the supposed inscriptions of the Israelites in the Gebel el Mokatab. The work was addressed to the Society of Antiquaries, and the author offered to assist an exploration in Mount Sinai, but the society took no steps in the matter. Edward Wortley Montagu, however, was induced to visit the spot and give an account of the inscriptions. The same year Clayton published 'A Defence of the Essay on Spirit,' London. His next work was 'Some Thoughts on Self-love, Innate Ideas, Freewill,' &c., occasioned by David Hume's works, London, 1754. The same year he brought out the second part of the 'Vindication of ... the Old and New Testament,' Dublin. This produced Alexander Catcott's attack on his theories of the earth's form and the deluge. In 1756 appeared 'Letters which passed between . . . the Bishop of Clogher and Mr. William Penn concerning Baptism,' London, in which he asserted the cessation of baptism by the Holy Ghost. Clayton's friend William Bowyer obtained a copy of the correspondence and published it.