It looks like the schematic will work but, personally, IMHO etc etc:
- I think you've got 3 fuses too many. Put a 1.5 or 2 amp fuse on the incoming supply on the left, followed by a diode to the first relay, with a "safe 12v" point declared at the pointy end of the diode and the relay. Connect all the other 12v points to the "safe 12v" point
- What's the 1n4001 diode at the bottom left for?
- I'd ditch the relay at the bottom left and the 3xAA batteries in favour of what you had before (a regulator) with a few suitable components around it to make it "automotive". Google for the Megasquirt power supply and base yours on that - that will be good enough
- Experiment with your motor - I would look at connecting it to 12v with a "dropper resistor" that drops 9v across the resistor at the current that the motor takes (others may not agree!). Then I'd ditch the bottom right relay and the 12v->3v adapter and connect the ground of the motor to OUT5 on the 2003, Don't remove the 0.1uF from the motor though.
Just $0.02 worth of course - but it just strikes me as too complicated than it needs be..