Hi Renae,
I have looked at this again and yes, as you said IGI has 2 Thomas's born around same time

I now think that as your Thomas did not name a son Samuel, it is unlikely that Samuel is his Father.
So that brings us back to Thomas as being the possible one.
The 1841 Census Suzard posted for you is the right one but she has accidentally missed off;
Elizabeth aged 9
1861 Census RG9/1850/74/4
16 Chantrey Lane
Quatford,Shropshire
Thomas OWEN,Head,mar,61,builder employing 14 men,born Cleo/Mort
Elizabeth,wife,mar,55,provision dealer,born Albbrighton Shropshire
Elizabeth,daug,unm,29
Thomas,son,unm,28,builders clerk
William,son,unm,21,joiner
Jane,daug,unm,18,? marker
Lucy,daug,unm,15,scholar
Mary,daug,unm,12,scholar
John POTTER,boarder,unm,25,civil engineers adjudant
All children born Quatford and John Potter in Hertfordshire
Marriage;
John POTTER
Fanny OWEN
September 1864
Bridgnorth
6a 999
1851 Census HO107/1986/393/7
26 Woodford Cottage
Quatford,Shropshire
Thomas OWEN,52, joiner- builders manager
Elizabeth,
Elizabeth,19
Thomas,18,builders clerk
William,11
Jane,8
Lucy,5
Mary,2
Nehemiah SPRATT,63,lodger,widow,joiner
John BEARD,29,lodger,mar,joiner
1871 Census RG10/2743/4/1
2 Waterloo Terrace
Bridgnorth St Marys, Shropshire
Thomas OWEN,head,71,retired builder
Elizabeth,wife,67
Elizabeth,daug,39
Arthur OWEN, sons son,3, born Bridgnorth
Trish