Dave, not necessarily. The coils do fire in pairs, but it is possible for one of the two wires to have a faulty connection at the coil, so one plug fires while the other doesn't.
Technicality:
If a connection is broken, both plugs with not fire because current can no longer circulate in the coil's secondary loop. If one plug is shorted, or one lead shorted to frame, then only one plug of the pair will spark.
Putting 750 coils on a 550 will not make it run or have the power of a 750. But, you will be more likely to have battery recharging issues, which itself can be impacted by many other factors.
do the spark plug boots go bad....?
They can, as anything that man makes can fail. The 550 plug caps should have 10K ohm resistance through them (+/- 10%). However, 5K ohm will work, too. The caps unscrew from the wires, if that helps.