None of your data fits with mine; however, have you exhausted the available Scottish records? After 1855, they are super. Have you looked for R.C. church records in Kilmarnock? They do not usually have staff to look for you, but will sometimes let people look for ancestors. My friend found some pertinent records in Dalry. If you can read all the birth, marriage and death certificates for your John's family, including parents & grandparents, you may learn something that takes you further back. I got the counties in Ireland from those kinds of records in Scotland over 20 years ago. They are much easier to access, now. There are some records for "McGinnis" in Kilmarnock in the GRO.

Good luck.
Barbara