This whole thing requires ignoring the fact that the change in regulations was made years after the ink dried on the M9 contract.
A completely new order can be drafted with something like the FLIRTs, ideally for the short LIRR branches and locals on the Hudson, Harlem, and New Haven branches (the M7s and M9s can instead be used on other routes). Of course, the cars would also need to be short enough to fit into the 63rd Street Tunnel, preferably without sacrificing the ability to use overhead wires.