Suggest you forget about Ancestry/FamilySearch/IGI for the moment. They are great as finding aids but they don't hold all of the actual records. Go to www.scotlandspeople.gov.uk and you will be able to view the originals of all the items you have marked as NY or ??.
<quote> G-G-gmother Margaret Sinclair:
P - In 1851 & 1861 shown born in BRACO; in 1871 and 1881 shown born in MUTHILL.</quote.
As Braco is in what is now the parish of Ardoch, but at one time was in the parish of Muthill, the difference in information in the census about Margaret's birthplace is easily explained.
If Margaret was alive and in Scotland in 1881, there should be a death certificate on Scotland's People which should confirm Margaret's parentage.
<quote> IGI shows the marriage for Archibald and Margaret in 1801 in MUTHILL and a son Archibald born 4th of April in MUTHILL. [I have read Muthill register without finding these]</quote>
These events are both in the index at Scotland's People. However if the Muthill OPR was reconstructed 40 years later the marriage date could be a guess based on the DoB of the child. Note that it mentions only the year, not an actual date.
<quote> NY - Archibald born 21 April 1782 in MUCKHART to Henry SINCLAIR and MARY SHARP. </quote>
If that marriage in 1801 is a guess, and Bettridge 1793, Donald 1795, Malcolm 1799, Archibald 1802, Margaret 1804 and John 1806 are all siblings, their father must have been born before 1782. If Mary b 1781 is also a sibling, then this Archibald is plainly not by any stretch of imagination her father.
<quote> 1799 March 24th Archibald Sinclair and Margaret McKENZIE in CLATHICK their child Malcolm" [this is the standard wording in this book and does not appear to suggest they were not married.</quote>
You can be absolutely sure that if they had not been married the register would have made it clear by describing the child as 'natural child' or 'born in uncleanness' or something along those lines.
Under Scots Law a woman does not lose her maiden surname on marriage. Until the early 19th century married women were known by their maiden names. Adopting a husband's surname is a relatively recent practice, but a married woman is described in legal and official records as 'xxx yyy or xxx' wher xxx is her given name, yyy her maiden surname and zzz her husband's surname. This is why you get the mother's surname in baptism records, and why the deaths of a married woman in Scotland is indexed by both her maiden surname and her husband's surname (or indeed the surnames of all her husbands, assuming that whoever registered the death knew them all).
<quote> NY - Archibald Sinclair & Margaret Sinclair Married 1 Aug 1774 COMRIE</quote>
This is irrelevant because Margaret's maiden name is Sinclair and your Margaret's maiden name is McKenzie.
<quote> Margaret Symore [sic] Mafterton Sinclair </quote> That isn't the letter 'f'. It is the 'long s'. It does look like 'f' but if you can compare it with a real 'f' in the same handwriting you will see that it lacks the cross-stroke.