I think your David was married twice. Firstly to Jane Cook on 20.9.1878 at Greenock Free Kirk. Then to Jane McKie in 1883. I don’t see a death for Jane Cook, in Scotland, so can’t say what happened to her. Parents on the 1878 marriage are identical, including father’s occupation of sawyer. So it looks to be the right man, and there seem to have been children by the first marriage. That 1878 marriage cert also says both parents were dead by that date. David was a merchant navy seaman in 1878. I see he later became a sailmaker.
You won’t find any records of people travelling from Derry to Greenock. Those were (and still are) domestic journeys and there’s no passenger information for that sort of route. There was an overnight sailing from Derry to Glasgow (Broomilaw Quay) 3 times a week, there were also daily sailings from Belfast, some of which stopped off in Greenock. Some also from Derry to Ballycastle and then on to Glasgow. It was a short and cheap route and folk went back and forth all the time. They went home for the harvest and for the Glasgow Fair etc.
If you can’t find them in the 1861 Scottish census, I suspect that the McIntoshes went back to Ireland some time between 1855 and 1861. Possibly Daniel stayed in Ireland. The Irish censuses 1861 to 1891 have all been destroyed so I can’t search there. I searched the 1901 Irish census but did not find him. (There was a Daniel McIntosh born in Scotland, in Belfast, Presbyterian, but he was far too young to be your family). I had a look for Daniel McIntosh marriages in Ireland 1871 – 1921. There was only 1 and it wasn’t your man. I also searched for a death and didn’t find that either.
Probably worth checking English censuses and death records in case the family moved there. If William & Sarah died in Ireland 1855 – 1863, there won’t be a statutory record as death registration only started in 1864.