Long Planned, Transit Projects Get U.S. Help
Transportation Dept Sec Mary E Peters announces final approval of $2.6 billion in financing for tunnel connecting Long Island Rail Road with Grand Central Terminal; link will bring LIRR commuters to Manhattan's East Side, saving as much as 40 minutes; Peters also announces $693 million in federal money for Second Avenue subway line; both projects have been in development for decades, although substantial work has been done on each; both projects are scheduled for completion in 2013 and both will require much more money to complete; photos (M)