#1 - how to get home: Don't make a plan until you get a couple of weeks from being done. It's so much nicer not to have a hard-and-fast deadline for where/when to finish. I did this for my XC, and was thinking I would buy a plane ticket (or train or bus) at the last minute, but then I ended up getting offered a ride home to California in a car. Yeah, that's not going to happen to everyone, but it shows how giving yourself flexibility allows you to take advantage of whatever comes along.
also, you will know a lot more at that point what you WANT - do you just want to get home, right away? do you want to mosey? do you want to ride your bike home? if it's about what's best for you psychologically, no one can answer for you. if it's about cost, don't forget to add up all the $ you will spend on lame train food while you are sitting around for days on the train. and the pain of sleeping in a train seat.
#2 packing for the bus: cardboard boxes are fine, you can get them for free at bike shops, (if you are lucky) or for $15 at the greyhound depot (also if you are lucky) or you can go to wallmart or whatever and make one out of regular cardboard boxes. you will NOT get a straight answer on the phone about whether a box is available at the bus depot. plus, the thing that i found so hard was if you get box somewhere else, you have to figure out how to carry your box/boxed bike from where ever you are to the bus. so then what, do you carry the box to the depot, and sit there and box it up, while you are waiting for the bus?
ugh, the bus sucks so much. train is the same.
try to find a different way. hitchike, post an ad on craigslist, rent a car or uhaul - seriously, this could be as cheap as a bus, i did this, there were 2 of us, and it was cheaper to rent a car one way than buy 2 bus tickets.