I'll take the first stab at your questions, although I'm going to have to admit, we'll need someone with a lot more knowledge than I have to really give answers... but on the under-running third rail, you are correct.

The New York Central installed under-running third rail on its commuter lines east of the Hudson River (the one line west of the Hudson River was never electrified, and eventually became freight only). The third rail is still in use, and in fact on another line, has even been extended further north in the last twenty years, by the New York commuter agency.

What's really interesting, is the diesels on the passenger trains here the same, Amtrak and Metro North both use a variation of P40/P42, called the P32AC-DM, to run through here, and they are both set to run off the third rail when they get into the tunnels in New York City.

The difference is that the Amtrak units go into Penn Station and the Metro North units stay on New York Central the whole way and go into Grand Central. Penn Station's third rail is over-running, from the orginal Pennyslvania RR electriciation, and the Long Island Railroad. So, the Amtrak engines have different shoes, I believe, than the Metro North engines.