I believe the problem is the thermistor sensor. On the thermostat housing there is a sensor that is connected to a two wire harness that goes to the injection pump; this is the "cold start advance" portion of the system so it starts easier when cold by advancing the timing.
When the sensor on the thermostat housing fails it shorts out and blows the fuse. Try unplugging it, replace fuse and see if it starts and runs. The part # is RE503242, if you are quick changing it, you don't have to drain the coolant, just make sure it's not hot at the time. You will want a pan under the tractor to catch the coolant, so as not too have to clean it up.
You may need to re-prime the fuel system, if it still does not start
To comply with the exhaust emissions regulation, the timing of injection pump should be around 6 to 9 degrees before TDC. These timing values do not allow proper start-up operations when engine is cold. To ease engine start-up, a cold advance system gives to the injection pump a temporary over-timing.
When coolant temperature is below 50 C (122 F), the solenoid valve is activated and opens the cold advance circuit.
URL to JD parts
jdpc.deere.com/jdpc/servlet/com.deere.u90490.partscatalog.view.servlets.HomePageServlet_Alt
URL on the 3029 engine and addresses the cold start
www.visaevolution.com/dati_sito/manuali/officina/motori/john deere/ctm125-3029-ENG.pdf
