Complex sentence: Around the same time that Mary was removed from his custody, Shrewsbury and Bess separated for good--they had been apart off-and-on since about 1580, and even Queen Elizabeth had tried to get them to reconcile.
Split into simpler sentences: Around the same time that Mary was removed from his custody, Shrewsbury and Bess separated for good. They had been apart, off and on, since about 1580; and even Queen Elizabeth had tried to get them to reconcile.