Only one cylinder has spark got a new ignition coil for the other cylinder now both dont have spark?

I unplugged the kill switch wires from both ignition coils now both have spark is it alright to run it with out the kill switch wires and just use the key to turn it off?

No...its not alright. Its there to kill the motor in an emergency. Find the problem and fix it.

The diode in the wire going to the coil that works has gone bad and back-feeding to the coil that has no spark. In emergency it is safe to run with just the 1 kill wire disconnected (the coil that has no spark when wire is connected) as long as your anti-backfire solenoid on the carburetor is still functional - when you turn the key off, or kill lanyard is pulled, the anti-backfire solenoid (closes fuel delivery inside the carburetor to the engine) and the 1 coil still connected to the switch(es) will shut the engine down...

The replacement wire set should be around $10-$15