Coils and magnets very rarely go bad. ... Coils will look diffrent depending on who makes them for the engine maker, the supplier may have changed..
The three / two magnet flywheels don't really mean anything, I have read that the third on newer engines may snap a spark to scavange unburned fuel, or to advance the timing (I can't lie to you , I don't know what your's is good for- if anything)...It may not even be used on your motor, It is cheaper to have one plant making flywheels that fit more than one motor/engine
Check for corrosion on the posts that mount the coil, clean the mouting areas witha piece of "Scotch Bright" ...
Did you check the resistance of the secondary on the coil to ground?, compare it to the running coil.?
It's not mounted upside down is it?
Have you tried to put the "bad" coil on the running unit?
Some coils have a Replaceable resistor in the plug wire cap... (Honda's do and others)... these are placed in the coil to supress radio noise, these resistors sometimes burn out...
Just a few things to think about,
Good luck,
Friiy