' I don't have information handy on the origin of the surname Johnstone, but would guess it derived somehow from a patryonymic - e.g. John's son - but the "stone" may have a special significance. It could well be derived from Johns 'toune', a scottish word for 'town'.
I do know that a Johnstone/Johnston Clan was one of if not the major Border clan in Scotland at one time. They were a large, strong, fortified, unintimidated and well-friended group. My Border Scots ancestors, the Irvings of Bonshaw were quite close with the Johnstones and they took one another's part in many a conflict.
There are several stories about the Border clans to be found on the internet and elsewhere and the Johnstones are probably mentioned in every one.
When James became King of England and Scotland, much trouble arose between him and the Border Clans. He wanted to be rid of them despite the many times they had aided him when he was King of Scotland. Many members of the Border families who were close emigrated to Ulster together and some others to America. The tendency for members of these families to marry one another continued to Ulster and probably to America as well.