On June 4th should I be able to buy a train ticket when I arrive in Madrid to Murcia? I should get into the airport at 9:45am. Take a taxi or metro? to the train station? should I take a bus to Murcia instead of a train?

Take the train, it's much more comfortable than the bus. You can also purchas a ticket on Renfe's Web site and just have the ticket printed at the station when you get there. They give you a ticket locator number and confirmation sheet so that's all you have to give the ticket agent at the station. (There is even a Renfe agent at Barajas so you can get it there as soon as you arrive).

The ride is about 4.5 hours and is about 55 Euros roundtrip.

I would recommend taking a taxi to the station. It's just easier than the metro that can be hot and crowded and seem excessively so with a heavy piece of luggage. I don't remember if trains to Murcia leave from Atocha or Chamartin, but either way, you'd make at least 2 train transfers to get to either.