I thought I was starting to understand it, but I'm lost again with the sequences of events. Maybe I'm trying to read too much into it.

If I followed it right, John Quark doesn't enter into the scene at Ballakilley until he purchased a part of it from Jo Cloage in 1682. That's a year after his (proposed) father in law Phill Moore died. In 1686 the entries for Ballakilley were Tho Moore Jr, Jo Quark, Phil Moore, Jo Kelly & wife, Sir James Moore (ref: earlier in the thread from Frances 16/10/2014 6:47pm). As the original Phil Moore didn't have a son named Phil, the one in 1686 must be another one.

If John Quark bought into it, as opposed to inheriting, then is there any reason to think he is related (through marriage or otherwise) to the Moores or to the Clagues who occupied the other parts of the land? I'm very confused here.

John Quark of Ballakilley died in 1689, as we know from earlier in the thread, with his unknown wife still alive. I'm not sure who was his heir. Perhaps his son John?