I assume this bike was running fine and it started to have this problem, and your not installing a new ignition system for the 1st time.
Yes, only one side of a
single fire coil can be bad.
Not the case with dual fire waste spark system. Since the 2005 is a single fire coil, it is two coils in one package. One side can be bad with other side being good..
As a test... What you can do is reverse both the secondary and primary sides to see if the problem is the coil or the ignition module that is driving it.
To do this,,,1st make a current diagram of what color wires are going where. Same with spark plug wires. Make a diagram
Now swap the two outside primary wires of the coil and leaving the middle terminal alone (that is the power lead).
Now swap spark plug wires in the coil output towers. (Pull both spark plug wires at coil and swap towers)
Start the engine. If the rear cylinder is still the only one that is working, the ECM or ignition module is the problem. But if the front cylinder now becomes the one that is working & the rear cylinder is the dead one,,, that tells you the coil is bad.