Pickup coil - If it is defective due to broken leads, shorted coil or open coil the bike won't run at all. If it is misadjusted it could cause the bike to run intermittently on one cylinder at times or run poorly.
HT coil - If the coil has an open primary or secondary circuit, the coil won't fire on that cylinder. You can check the coil with an ohmmeter or megger. The problem usually doesn't go away. If the coil is shorting, the problem on that particular cylinder could be intermittant just like the pickup coil. If switching coils from side to side causes the problem cylinder to follow the coil, change the coil.
To check the pickup coil, use an ohmeter across the leads to determine what the resistance is. I don't remember what mine is so can't help. It shouldn't be infinity nor should it be zero resistance. To check adjustment, you have to pull the triangular side cover off the rt side of the engine and measure with (Should be non conductive) feeler gauges. .8mm is the measurment.