If you think you'll only use the subway in NYC a couple of times a day then i wouldn't bother with a daily pass, further information on subway fares and the advantage of using the pay-per-ride metro card and pay $2.25 per journey (get an extra 7% for every $10 deposited) vs paying $2.50 for a single ride ticket
Use the Amtrak status maps to check if the train is running behind (or not)
http://www.dixielandsoftware.com/, the train from Flagstaff to LAX is the South West Chief, so using the status map would be found in the 'west' as train number 3
+1 on taking the direct flight
