Hello Amy,
Welcome to the wonderful world of Rootschat!

I looked through the pre-1855 Monumental Inscriptions for St. Ninians but couldn'd find a match for John Stewart and Janet Thomson.
Male Stewarts listed are:
1.
W. Stewart 1848
2.
Andrew Stewart died 4th April 1863 aged 64
His wife Margaret Hodge died 6th May 1892
Son John died 26th February 1916 aged 73
His wife Janet Cunningham died 17th November 1934
Their son William died 2nd September 1902 aged 17
Thier son James died 23rd April 1917 aged 33
3.
John Stewart & wife Helen Jaffray (1829)
Do any of the above fit in to be your couple's children?
Anne