I was looking at the NWL wills yesterday too but got a little side-tracked by my other 'Morgans' family ( Llanfihangel Rhos y Corn and Llanybydder ) There were quite a few interesting connections in one Morgans Will but not enough to establish any direct relationship.
As regards the Morgan family at Newchurch/ Llanpumsaint/Abergwilli I will give you the information I have. I have traced my family back to John Morgan b Abt 1796 . His father was Richard Morgan, a gentleman farmer or as described on one of the marriages of John, a Gentle-farmer! John was my Gt Gt Gt Grandfather His first marriage was to Margaret Jones - my Gt Gt Gt Grandmother. I have the Parish Record of this marriage and the witnesses were Oliver Morgan and Wi ill? John. The marriage took place at Llanpumsaint in 1817. Margaret died in 1836 at Llangwilly/ Glangwilli, Llanpumsaint and his 2nd marriage was to Ann. She died 1845 at Pentrefynys, Abergwilli . John's 3rd wife was Sophia Thomas, a widow.I have their marriage certificate and the witnesses on that are Richard Morgan and David Davies. They married at the PC Conwil in 1850. Sophia died 1885. I am wondering if John could be a brother of your Thomas. One of John's son's farmed at Bwlchyronnen Abg. 1861 census His name was Richard.
I can give you further information on the family of John Morgan and the various abodes.
I hope this information doesn't add to the confusion!
Best wishes,
Maureen