Complex sentence: The nave and the tower (south of the nave) were rebuilt in 1840; the rebuilding used the original foundations, and so the chancel is not quite aligned with the nave, being slightly to the south.
Split into simpler sentences: The nave and the tower, which is south of the nave, were rebuilt in 1840. The rebuilding used the original foundations, and so the chancel is not quite aligned with the nave, being slightly to the south.