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I checked Roots Ireland for Co. Waterford and did not see a Thomas Keller baptismal record from 1788-1804. Most of the Co. Waterford RC parishes do not have records back to the late 1700s/early 1800s. If Thomas was not RC, Roots Ireland does not have any Church of Ireland or Presbyterian records for Co. Waterford.
You may want to post Thomas' story on our XO Chronicles site https://www.irelandxo.com/ireland-xo/history-and-genealogy/ancestor-data...
You may also want to consider autosomal DNA testing.