The parish boundaries around Grandtully are extremely convoluted, with small detached parts of several parishes close by - Dull, Weem, Little Dunkeld and Logierait.
According to Fullarton's Gazetteer (1842) Grandtully is a district partly in Dull and partly in Little Dunkeld, so there is no conflict between Grandtully in one record and Dull in another.
Upper and Nether Pitcairn are both in the Dull part, so again there is no conflict of places.
If the witnesses to John's baptism were 'the congregation' then he was indeed baptised in the church, and if the day of baptism was a Sunday, it's likely that he was baptised in the church, but otherwise probably not, as it was not unusual for a baptism to take place in the parents' home.
John Stewart and Grizel Farquharson had four recorded children: John 1823, Alexander 1826; Margaret 1828; Grizel 1833; all baptised in Dull. You can and should look at the originals of these baptisms to see if they list the names of witnesses who could be clues to family relationships.
In the 1851 census there is a household at 179 South Street, Perth, comprising John Stewart, 55; Grace Stewart, 55; Margaret Stewart, 22; and Grace Stewart, 17; all born in Dull. The given names Grace and Grizel were used interchangeably in Scotland, so these are your John's parents and sisters. In 1841 they were in the village of Guildtown in the parish of St Martin's, but that listing doesn't provide any extra information.
In 1861 John Stewart, 62, and his wife Grace F Stewart, 62, both born Dull, are in High Street, Perth. There should, therefore, be death certificates for both, which should tell you the names of their parents, assuming that the informant knew this, of course.
It won't have escaped you that they were a bit inconsistent with their ages. Age 55 in 1851 implies a birth in 1795/1796, and age 62 in 1861 implies 1798/1799, therefore at least one of these pairs of ages is wrong. (In 1841 they said they were 40. Adults' ages in 1841 were supposed to be rounded down to the nearest 5 years, so that implies that they were born between 1796 and 1801.)
Grace Stewart or Fairley, mother's maiden surname Farquharson, died in Glasgow in 1895 aged 62. This might be your John's sister.
The originals of all this information are available to view at
www.scotlandspeople.gov.uk at modest cost.