You are up against a couple of problems. Firstly, McFadden is a very common surname in Donegal. In the 1901 census there’s 574 (mostly RC). Secondly, very few RC parishes in Donegal have any records for around 1803. (Most start in the 1820s or later). So there is a possibility that even if you knew exactly where Robert was born, you might not find any documentary confirmation of that.
If Ellen was Episcopalian, that’d be the Church of Ireland. A mixed marriage in the 1820s/30s would, in my opinion, probably have taken place in the Church of Ireland, rather than the RC church. (I think RC canon law prohibited it until about 1834 but am open to correction on that).
The Church of Ireland does have some records that go back further than the RC church, but unfortunately many were lost in the 1922 fire in Dublin during the civil war.
331 Crawfords in Donegal in the 1901 census, mostly Church of Ireland.
You mention that Ellen McFadden was born in Leck, Co Tyrone c 1826. That’s quite a distance from Donegal but perhaps the family moved. The RC parish records for Leck (RC parish of Donaghenry) start in 1822, and are on-line free. You can check them on this site:
http://registers.nli.ie/parishesThe Church of Ireland records for Leck (Parish of Ballyclog) start in 1818. They are not on-line anywhere, so far as I am aware, but there is a copy in PRONI (the public record office) in Belfast.
Most farmers would be listed in the tithe applotment records (a form of land tax). Not all the tithes for Co Donegal survive but those that do contain 9 Hugh McFadden households, in the period 1825 - 1834. (Search under McFad* to get all the variant spellings). Each shows the townland where the person lived and their parish. You might want to use that as a way of narrowing your search a bit. (It does of course assume Hugh was still alive when the records were compiled).
http://titheapplotmentbooks.nationalarchives.ie/search/tab/home.jsp
