First and most important. I hope you are mistaken, and that you have one breaker. You cannot have separate breakers for this, you need a single breaker.
The proper and best solution is to replace the existing cable with a new cable containing four wires. Is this possible?
Follow the directions that came with the cook top about connecting it to a three wire connection. These directions will tell you about bonding the shell to the neutral wire.
Most cooktops and ranges have instructions for both three- and four-wire hookups. Follow the instructions for three-wire hookup. If your cooktop does not have instructions for three-wire hookup, then you need to either run a new four-wire cable or find a new cooktop.
__________________
Good luck with your project!
-Ben
Installation instructions :
"Frame grounded by connection of grounding lead to neutral lead"
Does this mean i can connect both the green insulated and white insulated on new cooktop to white wire of old?
Previous top had un insulated ground to white wire of existing.
Is there a method of checking whether the exising cable and metal junction box is grounded?
If so, could the green wire be attached to the flexible conduit or the junction box?
> Does this mean i can connect both the green insulated and white insulated
> on new cooktop to white wire of old?
For three-wire installation, yes.
> Is there a method of checking whether the exising cable and metal
> junction box is grounded?
With the power to the circuit off, use your multimeter or ohmmeter to check for continuity between the white neutral wire and the metal box. Your metal conduit may actually provide a suitable ground. Can you identify if the existing cable is individual conductors in conduit or BX cable?
> If so, could the green wire be attached to the flexible conduit or the
> junction box?
It would be connected to the metal junction box by way of a self-taping green ground screw (available in the electrical aisle).
__________________
Good luck with your project!
-Ben