Hi that is correct, given that a 20amp fuse is blowing instantly you have a dead short to ground. You have said the fuse doesn't blow if the yellow wire is not connected so therefore the yellow/red and everything before it (kill switch, Ignition switch etc) must be ok.
The fault can only be the yellow wire to the new coil (possibly damaged in the clamp as Mikaw said) or the new coil itself is faulty.
By testing the yellow wire with it disconnected from the coil and the yellow/red wire you will identify if the fault is in the yellow wire ( which is unlikely given that it is new)
You can carry out these tests with the switch wire (points wire) disconnected as you will need to disconnect it anyway for the next step of the test if the yellow wire is ok. The points wire cannot blow a fuse directly as the points switch an earth so it is going to ground anyway when working correctly whenever the points are closed.
The reason for testing the points side of the circuit is to make sure this is not why the coil has failed before you replace it. A coil is designed to be switched "on" & "off", if it stays switched on (points are closed up or points wire is shorting to earth) the primary winding in the coil will heat up very quickly (like a light bulb filament) the coil is normally oil filled to help keep the heat under control but can after 10 minutes + get so hot the winding burns out. When this happens it can create a dead short inside the coil. This is why the kill switch should be off until you are ready to start the engine. Hope this helps