I've found a record of burial of a John Caveen for 28 Jun 1788 in Arbory - I assume this is John, father of Richard who inherited the assets of his father as per the letter you posted?
What I have found on Family Search is that Thomas Caveen's (b.Jul 1782) father was called Richard, who was married to Elizabeth. They also had a daughter called Elizabeth ch. 17 Aug 1777 in Arbory. There are no records for other siblings.
You wondered if this John -Richards father and grandfather of Thomas (b. Jul 1782) - was the BROTHER of Thomas (b. Dec 1725) who married Cath Cubon?
The family tree I have constructed for Thomas is as follows:
his father was William Caveen b.1686 and mother was Isabel Waterson (1689-1748) - marriage was 29 Oct 1709.
Children for them as follows: John (1) b 22 May 1715;
John (2) b.28 Jan 1723 d.13 Sept 1733;
Elizabeth b.1712 Malew;
Joney b.22 Feb 1718 d.24 Feb 1718 Malew;
Elinor b.28 Sept 1729 Malew;
Henry b.5 Nov 1732 Malew - who married Elizabeth Bridson (nee Clark) 3 Feb 1761;
Thomas b. Dec 1725 who married Cath Cubon
If, and how, John - father of Richard and grandfather to Thomas who married Catherine Harrison - is connected to Thomas who married Cath Cubon I don't know?
I have traced back from William Caveen b. 1686 and identified his parents as John Caveen (1656-?) and Issable Vandie (1656-1692). They also had Margerie b.1682 and John b.1684. Maybe 'our' John' is a descendant of theirs??
Very interesting and very confusing.