The 1000v rating is the PIV or Peak Inverse Voltage rating. It has nothing to do with the "12V system". That is the voltage the diode can stand up to in reverse bias mode.
Voltages like that can easily be generated in 12v systems, caused by load d umps, normal variations in switching on/off loads like motors & valves & so lenoids, etc.
Generally a higher PIV rated diode will cost you more. There is no harm in using a diode with a higher than required PIV rating. But whether or not it 's needed at all in your system is a question.
I can't see why you would need a 6A diode for the excite terminal. That ter minal powers the field winding until the alternator is spinning fast enough to power itself. It generates the magnetic field. 6A is an awful lot of fi eld strength. You should base your diode selection on the alternator you ar e using, not the tractor. Research your alternator.
Often there is no diode -- in fact typically there is just a light on the d ash tied to B+ -- your "charge" light -- that provides the excite current w hen the key is on and the alternator is not yet turning. Once it's turning, the voltage on that alternator excite terminal rises to the B+ voltage, th en you have B+ on both sides of the lamp, and the lamp turns off.
Maybe the diode is there to prevent current from flowing out of the alterna tor back to the ignition circuit -- but I fail to see the harm if that happ ens unless the voltages are very different. If you have no charge lamp, a s uitable resistor will provide the same function, and limit current in that circuit.
Do a little more research before you believe everything you read or hear... . and I'm sure you can come up with a suitable solution.