Susan, found the birth/baptism on IGI of the James Gilmour bc1839 married to Jessie and looks like he can be discounted as parents given as David and Elizabeth.
The others listed with Thomas Gilmour, Manf (poss Manufacturer) in 1841 were, Agnes 30, Archibald 14, John 14, Thomas 15, Thomas 9 and William 12 - it doesnt give relationships to head of household. Note two Thomass listed and also was Agnes old enough to be the Mother of eldest children? James may have been born just after the 1841 Census??
Just a few other points of interest - John Gilmour bc1826 looks like he was later a Muslin Maunufacturer, born Renfrewshire but moved to Glasgow. There was also an Agnes Gilmour bc1811 (maybe Thomass' wife?) on 1851 Census, an Annuitant, also listed as born Renfrewshire living 4 Newton Street, Barony, Glasgow, Lanarkshire. Same address in 1861 but birth year 1807 and 1871 Census she was living at 10 Newton Street and gives her birth date as 1806. (But no James living with her on any unfortunately).
Archibald aged 14 in 1841 could be the one listed as a Mason in 1851, lodging in Stirlingshire. Also found an Archibald Gilmour bc1787, perhaps a brother of Thomas? born Paisley, Renfrewshire occupation Silk Merchant. I think I also saw a William Gilmour, Silk Merchant.
Obviously it may not even be correct family as James cant be found on any Census with them to connect him but the Marriage Certificate for James and Julia does give his Father as Thomas, occupation Manufacturer and the areas they were in also correspond with the other birth/death details you have.
An idea may be to join the Rootsweb list for Renfrewshire and Glasgow to see if anyone can help you on there. There may also be Parish records you can check?
Sandra