You should contact the University of Glasgow and equire about their archives for Rev. John Thomson. You can access it here: http://www.gla.ac.uk/services/archives/collect/university/
And the University of Edinburgh here:http://www.ed.ac.uk/schools-departments/information-services/services/library-museum-gallery/crc/collections/special-collections/eua
Have you checked this link? http://freepages.genealogy.rootsweb.ancestry.com/~sassytazzy/family/surnames/thompsonjohngennotessogrl.html
There are a number of records you could check the the period in question. These relate to County Down.
1708 Householders in Downpatrick town. 'The City of Downe', R. E. Parkinson
1720 Down and Antrim landed gentry. Royal Irish Academy 24 k 19.
1722-1970 Records of Southwell Charity School Downpatrick. PRONI (Public Records of Northern Ireland), D/2664.
1740 Protestant Householders (Partial). PRONI T.808/15258.
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Genealogist (Ireland XO)