You can have the coil for 1 and 4 going to plugs 1 and 4, but that doesn't mean wire #1 HAS to be on plug #1. These bikes run on a "wasted spark" setup. Both #1 & #4 plugs fire at the same time, since one is on the compression stroke (in which case the plug will ignite the air/fuel charge) while the other is on the exhaust stroke (in which case the plug will be sparking into a cylinder full of exhaust gasses and do essentially nothing). Cylinders 2 and 3 work on the same principle. So, plug wire #1 can be on plug #4 and vice versa, and the engine will still run fine.
The wires that must be properly connected are the ground wires connected to the points. The blue wire triggers the coil for cylinders 1 and 4, while the yellow wire triggers the coil for cylinders 2 and 3.
Both coils are exactly the same, so in theory (for example) you could use a "1&4" coil for cylinders 2 and 3, provided it was triggered with the yellow wire (despite that it has a blue wire coming out of it).