Complex sentence: He spent his first few years establishing his authority over recalcitrant clergy and congregations who resented this Episcopal "upstart" and who thought they still owed allegiance to the Bishop of London, the person responsible for the supervision of overseas Colonial and Consular Chaplaincies.
Split into simpler sentences: He spent his first few years establishing his authority over recalcitrant clergy and congregations. They resented this Episcopal "upstart" and thought they still owed allegiance to the Bishop of London, previously responsible for the supervision of overseas Colonial and Consular Chaplaincies.