Work to strengthen and modernize Muni’s Sunset Tunnel will end up costing $4 million more than planned — due in part to neighbors’ complaints about noise and late-night work. The Municipal Transportation Agency board voted Tuesday to approve the additional payment to contractor ProVen Management, for a total of $23.3 million, because of delays, mostly associated with neighbors’ appeal of a night work permit, and additional work requested by the agency. Opened in 1928, the 4,232-foot-long tunnel, which carries the Muni Metro N-Judah between Duboce Park and Cole Valley, needed repairs.