Hello again Nick,
Thank you for posting all that information.
1. I agree with you that the 1854 entry - from the Old Parish Register of the
established Church of Scotland in New Monkland, Lanarkshire - for a marriage between Jane BROOKS and James MIGRANSCHER is surely yours.
As Monica has suggested, if you download a birth certificate from ScotlandsPeople for one of the younger children, it should give the date and place of the parents’ marriage (which would presumably confirm or disprove that the record is your people).
The ‘What’s in the Database’ section of the ScotlandsPeople site indicates what details are given on a Statutory Register birth certificate; to quote from the SP site:
"Couple: date and place of marriage – 1855, then 1861 to date".
You might also wish to download from SP the OPR entry for the 1854 marriage to see whether James’s surname is just a transcription error.
2. I definitely agree with Tom that the age given for Jane (BROOKS) ‘MCGRANTHIN’ in the 1891 census – 33 – is just an error (probably a transcription error) for 53. That is, she
is Edward’s mother and the grandmother of young John. Note also that her birthplace is given as Glasgow (as it always is for Jane snr) whereas Jane jnr was born in Shotts.
3. Jane and Jean are interchangeable and are even combined in the IGI i.e. a search for a Jane will bring up all those named Jean as well. And yes, at times – though less commonly in my own experience – a Jane/Jean will be recorded as Janet. Also note that a very common alternate in Scotland for Janet is Jessie – so you will need to consider that as well in your searches for Jane (BROOKS) MCGRANNATHAN prior to her marriage, and in your searches for her parents.
4. It does rather look as though grandson John SUTHERLAND and grandson John BROOKS are one and the same person

I guess you could search on SP for his birth certificate (under either name - and also, in case he was illegitimate, under MCGRANNATHAN or variant) and download it to see if it gives any clues.
5. My Irish ancestors came from Northern Ireland, so I guess they were Protestant, that would explain that I don’t have problems finding them in the Scottish records!
Sorry, but no, it wouldn't!
The reason you have found all the births of the MCGRANNATHAN children is because they were born after 1855 and thus they were registered in the civil Statutory Register which commenced in 1855 (it's nothing to do with their religion).
The reason you have found the likely marriage of James & Jane is not simply because it was recorded in a Protestant (in the general sense) Register but because the marriage was entered into one
quite specific Protestant church register; namely into an OPR (Old Parish/Parochial Register) of the
established Church of Scotland.I'm happy to expand further but hope you don't mind if I suggest that you first re-read my earlier post (reply #6) and look at the link which I gave (the
established Church of Scotland is represented by the straight line at the far left of the diagram on that site).
I am stressing this because it is such a very important point in relation to your search for a baptism for Jane BROOKS, and in your search for her parents.
Best of luck,
JAP