No spark - Fuse blows when connecting new coil wires??

My only q is step 1 says yo measure voltage between battery and disconnected yellow wire. Then step three says to also measure voltage between that and yellow wire. Are those two steps different and I'm just reading it wrong? 

Hi, in step 3 you are measuring the disconnected yellow wire with it also disconnected at the coil terminal, this will tell you if it is the wire or the coil that is faulty (don't forget to connect your meter to the + battery terminal as you are looking for a ground that shouldn't be there)

I understand. 

Just for clarity... The yellow wire is the one coming from the new coil and the yellow/red is wiring going to ignition/engine stop switch. 

So step 1 and 3 involve only the yellow wire from the coil-not the yellow/red wire, right? Would I do this with the wire to points also attached to coil? 

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

RSimaoh10,

Check your coil.

Disconnect the primary wires(+12v and points wires) from your coil(leave the coil mounted on the bike though) and measure the resistance of the primary terminals.

Meter on ohms.
One probe on the coil 12v terminal
Other probe on the coil points terminal

What is your resistance?
It should be at least 4ohms
 

Thanks wookie I'll check out your method.

F64 - so I checked the coil when I first got it. I checked it with the meter going to the ends of each wire. The resistance was fine and within spec. I have not tested the probes straight in the terminal without wires though. So I'll do that. 

When you've got your ohmmeter out measuring between the coil terminals, also check between the positive terminal and the mounting lug. The coil resistance may be ok but if it is shorting internally to the lug this is what will blow the fuse.

Thanks for the photo, I try to solve a similar problem