So your Mary is listed on later censuses (ie after her marriage) as having been born in Ireland? I have also found a Mary Roberts in 1851, age 14, born Ireland, lodging with a McGuire family at 61 Drygate Glasgow St Mungo district, and working as a Mill Doffer. Interestingly, a Margaret Roberts, age 20, born Ireland, occupation Flax Reeler is lodging at the same address. Perhaps an older sister? I would have to say that I do not see an obvious entry in 1861 for this Mary.
As far as Mary/Matilda is concerned - I really have no idea. Seems odd to call a child Matilda then refer to her as Mary, particularly if you already have a Mary! But who knows without the birth records.
The George born in 1850 is certainly listed as George and Jane's son. And hopefully Henry's son George, will have a birth certificate if you chose to download it at some point. Without the facts, you imagine all sorts of things.

Again, the easiest way to find James Ferguson's parents would be to download his birth certificate, rather than speculate.
Just to say in passing - I certainly got a few births for Jane Bailie come up on Irish Roots, so hopefully once you have her death certificate on SP, you will have enough info to find the correct entry. Good luck!