Here’s a simplified version of @KK 6 Ave Local‘s plan because I really liked that plan:
from Fordham Road to Bay Ridge via 3rd Ave, SAS, Nassau, and 4th Ave via Montague
from Jamaica-179th Street to Brighton Beach or Coney Island via QB, Bypass, SAS, Manhattan Bridge, and Brighton Local/Express (It will run both like the old as the is deinterlined to West End and the are to Williamsburg)
to LGA and Fulton
to the Jamaica Line past Broadway Junction
in Queens Blvd express via 53rd, local via 63
to Metropolitan, to Bway Junction
Basic deinterlining plans in most places, just becomes