Yes, Ferguson is a clan surname. It was the 38th commonest surname recorded in the Scottish birth indexes in 1990. Thomas is a fairly common given name so it is not surprising that there are numerous Thomas Fergusons. This does not mean that all of them are related to the wife of James Proctor.
You don't say where you are finding all these Thomas Fergusons, but whatever you do, never believe anything you find online other than an image of an original document.
As for the workings of clans, forget it. At best it will continue to confuse you, and at worst it will actually mislead you. Work back step by step from the known to the unknown.
You have the marriage record of James Proctor and Jean Ferguson on 20 July 1776 in the parish of Dunkeld, in the County of Perth, also known as Perthshire. Does this record include the name of Jean's father? If not, be very suspicious of any 'source', especially a second-hand one, that purports to name her father without any further evidence.
I see that neither SP nor the IGI lists any children of this couple. What independent evidence (i.e. evidence other than what is in the tree handed down to you) do you have to suggest that your ancestor is a child of theirs?
You wrote
I found the record of my "earliest Ancestor' James on ScotlandsPeople.uk so I believe that and the fact that my data and the online data both cite the same date, 5 Sept 1742, one as Birth (on my record) and one as Christening (on ScotlandsPeople) leads me to think this 'might' be family. I am looking for other proof and any data to the contrary will be considered.
Unfortunately this isn't robust, and it certainly isn't 'proof'. It is quite possible that someone else has found this baptism in 1742 and assumed that, because it is the only James Proctor in the right sort of time frame, it must be the right one. This is an assumption you cannot reliably make, and presumably you can't ask the person(s) who compiled your handwritten tree how they arrived at their conclusions.
You say that you have obtained certificates from the GRO in London, so presumably your Proctors must have moved to England? What is your earliest reliable sighting of them, and how do you make the connection back from there to Dundee or Dunkeld?
If you can let us have a few actual facts to get our teeth into, we might be able to help you get back a bit further.