1. The Council is a different internal body to the general meeting of the company. Once you have two members present for a general meeting, then you can transact whatever business you want. There is no need for a third person in this situation. So, you are not acting inquorate having only two people present at any meeting of the company. So any decisions made in general meeting are fully lawful and you don't need a third person. It is the general meeting which runs the company. So long as you have two people present when you meet once a year, this then is a general meeting and fully lawful.
2. I don't think you have anything to worry about here. So long as you clearly meet in general meeting you don't have problem. So, I don't believe you need to change things.
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4. The same Companies Act, 2006 applies to England & Wales as well as Scotland. So, the law is the same in Scotland as in England.