I suspect a bad/damage control station (valve) or wiring. You'll need to isolate each station and master valve to identify which valve has the problem. Try disconnecting all valves at distribution center. Then manual enable master valve and or station valve. Repeat procedure multiple times to identify which valve is causing fuse to blow.
If the fuse blows with all valves disconnected, then disconnect all valve at the timer and enable all the stations. If fuse still blows, the problem is in the timer. If fuse doesn't blow, then reconnect and enable each valve at the timer, one at a time to identify which circuit is bad.
Make sure that the transformer is supplying the 26 volts ac required by the pump relay and zone solenoids. If the voltage is there and unit still will not operate then the electronics are to blame.
