2004 FZ6 won't start

I need some help/ideas with my 2004 FZ6. It had a dead battery so I charged it using a trickle charger and it still wouldn't start. Now the check engine light is on and it displays a code 12. The battery that died was the original battery so I figured it was trashed so I replaced it with a new one thinking the code was probably due to the low voltage from the bad battery.

With the new battery the bike still displays the same code and check engine light and won't even attempt to start when I push the starter button. I've checked the fuses and they're fine.

Any thoughts?

Thanks

Can we get a little history on the bike? Has it been out of commission for a while, running okay and this just started? If I remember correctly error #12 is the crankshaft position sensor. It tells the ECU where the crank is for timing of fuel injection and spark.
One of our members had high mileage on his bike and the cam chain cut through the sensor. Have you been having loud cam chain noise? Sometimes a component just fails or a plug just comes undone.
Right side of the engine, lower cover....

Here: http://www.600riders.com/forum/garage-mechanical-help/40624-error-code-12-a.html

+1 on more history with the bike,IE: ridden daily, just purchased, mileage, maintainance, etc would help...

To elaborate on Ciffs post above:

Fault Code: 12
Diagnostic Code: --
Symptom: No normal signals are received from the crankshaft position sensor.
Probable cause of malfunction:
Open or short circuit in wiring harness.
Defective crankshaft position sensor.
Malfunction in pickup rotor.
Malfunction in ECU.
Improperly installed sensor.

Re your new battery,

Can you post the voltage across the terminals as it sits?
Does it spin over and not start or not spin over at all?