This is a huge undertaking. 9 volumes. And it may be a while before we get to it. But from what I've read so far in other sources, many Sinclairs/ St. Clairs were involved. In particular, those in the southwest of Scotland. I'm only searching those records from 1655 - 1688, which is not the entire duration of "the troubles." However, the later years were the most brutal, eventually to be called "The Killing Times." More records would have been kept, more trials. Also, it would have impacted our Alexander and his parents directly from 1655 onward.
This should whet your appetite -
Roland William Saint-Clair's "St. Clair's of the Isles" mentions a George Sinclare, Professor at Glasgow University. 1654 - 1696.
"George Sinclair or Sinclare, brother of the Rev. John Sinclar, Regent of St. Andrew's , elected Professor of Philosophy in the University of Glasgow 1654, and ejected in 1662 for refusing to comply with the episcopal form of church government, was restored in 1688, and retained his professorship (to which in 1691 that of mathematics was added) until his death in 1696...." He was a Covenanter !
Much more is written by Roland about this George, but nothing about any children. If you check the Poll tax records on the main page, under 1st person research, you'll see there's a George living in Kilbarchan. I do not know if this is the same George, but I find this professor's timing very interesting. He was thrown out of his job 4 years before our Alexander was born. He was not re-instated until 1688, when our Alexander would have been 12 years old. What did this George do in the meantime? Did he work? Did he make enough to send his kids, if he had any, to school? Would a son have decided in 1696, after his father died and left nothing, to leave the country to seek his fortune elsewhere. By the way, George is a family name, though not a prominent one.