Motercycle powered circuit advice and review

That 100 Ohm resistor is going to mess you up... Calculate the voltage drop across 100 Ohms at 260mA. :wink:
[EDIT] Tom beat me to it! ...You're not going to get 5V out of the regulator or 260mA.

Short-duration power dissipation shouldn't be a problem, but a short-duration voltage spike could still damage the voltage regulator (if you didn't have the Zener). We really don't know what the Zener will be exposed to, but if it fries it will probably short, protecting your Arduino. The series resistor may then burn-up and open (depending on it's power dissipation and rating), or you can add a fuse.

(U1) should be disappointing 1.61 W.

Dissipating. :wink: You'll need a heatsink.

...I've used an Arduino in a vehicle just using the Arduino's on-board regulator with no problems. I'd be inclined to just try the 7805 and see how it goes... If it burns-up go "back to the drawing board". Try it on the scooter with just some LEDs or something to see if it gets killed by a voltage spike.