As the kitchen and bathroom are landlords fixtures ( yes I know you bought the flat,m but they are) you carried out alterations which needed consent not to n#mention building regs approvals for alterations to services and any relevant certification to electrical and gas alterations.
Moreover if the lease is specific in the layout, and a landlord can argue its implicit that it should not be altered as, at the end of the lease, it should be returned as originally "sold", that a change of layout also needs consent.
If there is plan in the lease that will flag up an issue to a buyer or lender who will want it altered before competing.
Put together a simple sketch and photos gather your documentation and apply for retrospective consent. You will be responsible for the landlords legal and professional fees.
Based on the information posted, I offer my thoughts.Any action you then take is your liability. While commending individual effort, there is no substitute for a thorough review of documents and facts by paid for professional advisers