I suspect that the NFC is unique to the device. Limited googling somewhat confirms this but not 100%.
As far as power there are several options but here is what I see as the best. Since you already have 12v power available on the bike, it is best to power the Arduino through a voltage regulator from your bike's 12v. As you noticed, there is a 5V and a 3.3V available. Since you will be starting with 12V it is best to use the 5V Arduino. You are going to be dropping a lot of voltage even so which is going to generate a lot of heat in your Voltage regulator. a 7805 regulator can be had from radio shack but you wull need a couple of other components to make it work. Google 7805 Voltage Regulator and there will be plenty of diagrams to built the circuit. You will need to use a heat sink on the voltage regulator. There is a mounting hole provided and I think you can get them at the Shack as well.
Once you have your 5V power to the Arduino, you are going to want to control your 12V system through transistors. They are very simple to use and can also be had from radio shack. You can get multiple transistors on a single chip if you need it. A transistor acts as a switch. You supply 5V activation signal from the Arduino and it allows 12V to pass through. This 12V is isolated from the Arduino by the transistor. It is very similar to a relay. In fact, you can use relays instead. There might be current draw concerns but since you should only be sending the ignition signal to the starter anyway, I'm fairly certain the starting current does not pass through the ignition switch. If there isa high current draw, it would be wise to use relays instead. You can find solid state or traditional electromechanical relays through Sparkfun.
One thing you will need to be cautious of. In order for this to work, the Arduino needs to always have power. This means there will be a constant drain on the battery. In order to minimize the impact of this, I would do two things. Include a manual switch that can kill power to the Arduino so when you put the bike up in the winter you can just turn it off. Also, look into low power sleep modes. There are multiple sleep modes that you can use on the Arduino that will dramatically reduce the power consumption. In order to use this, you will need to pick up the read pin on your RFID reader. This will send a signal telling the Arduino that it has data coming. Attach this to an interrupt pin that wakes the arduino and you are in business.
Also keep in mind that your existing start button will have to be wired into the circuit to allow for an either or situation.
I'm sure you have already considered this but the Arduino needs to know when the bike has started. For example, you turn the key push the start button until the bike is running then let it go. the Arduino won't know when to let it go. Your initial thought may be to hold the phone close until it is running and then move the phone. But what happens when you accidentally get the phone in range when the bike is already running. This would wreak havoc on the starter so the Arduino needs to know when the bike is running so that it disables the start circuit. Feedback from the bikes alternator circuit or voltage regulator might be the best method. However, remember that the Arduino can only take a 5V input so a voltage divider might be used to step the voltage to the arduino down to usable levels. An analog signal is what you are looking for. Using this method might depend on how the voltage regulator/alternator circuit works on the bike. If the VR is putting out voltage while the bike is starting then this won't work.
Once all of that is working, the next thing to do is get rid of the key as well. Since you can't always leave the key in and on, at this what you are building is actually slower than the existing start system. If you can use bluetooth or wifi to tell the phone to 'turn the key' then use the phone to start the bike, that would be awesome.
And while I am at it, you might be wise to include a way to add a new 'authorized' NFC tag. What happens if you lose your phone. Short of re-programming the Arduino, while admittedly simple, it would be much cooler if you could but in a safe way to add more devices. For example, with the key on, the horn button depressed, and the left turn signal on (pick these signals up in the Arduino) if you scan a device that is not already in the system, it will add it. In theory you could add any 13.56Mhz RFID tag this way. Store this data on EEPROM which is insanely cheap and easy to use.
I will close my rambling with a note of encouragement. I am an avid VB.net/C#.net programming. While I have taken a single semester class in each over the years, I am almost entirely self taught. I have found that having a goal makes learning that much more fun. While I am still a novice at C#, I am a professional level VB.net programmer and enjoy making money on the side with it. Next I'm on to Java for Android and Unity3D. If you can make this all work, you will have expanded your knowledge dramatically and will quickly be looking for what you can do next. I am currently building a Time Machine prop for my wife's children's choir using Arduinos and Xbee's so I can control it remotely from the audience!