From what I've been hearing over time, is that the LIRR tunnels for East Side Access are basically the same vertical clearance as the 63rd Street subway tunnels above them (meaning even the overhead-equiped EMU's are too tall for them). Seeing as these tunnels (specifically the prefabricated sections that were placed into the East River crossing) were designed in the 1960's that's just... headdesk-inducing.
---PCJ