Its strange that there is no birth for Mary no 1 but there's a death registration, makes you wonder if Jane and Mary weren't registered at all, but then if you've checked the original church records it doesn't look as if they were baptised either, unless its was later than the dates you checked.
If Mary no 1 was Jane's twin, then Jane and James must have had 3 sets of twins as it looks like Robert had a twin brother as well!
Also in Ladyhawks post regarding the Mary who married James in 1860's, if its the right family - the lodger was called O'Neill - another relative!!!?
If Jane was an O'Neill is it possible that she's Bridget's (Batholomew's wife) sister?
Theres a James Keenhan marries a Jane Keenan in June 1868, could this be Jane Jnr, although she would only be 16 if the 1852 birth is the right one