81 kz550 dead on 2 cylinders

Hook up light to low voltage coil wires and see if it blinks.
You can attach 2 low wattage bulbs to side of speedometer (use masking tape) and connect them to each coil primary wires. The bulbs will keep blinking when bike runs OK. If you have a problem before ign. coils, one of the bulbs will stop blinking.

nickleo373 wrote: It's been a couple weeks since I've had problems with the bike but yesterday I turned it on and let it warm up in the driveway. About 2 or 3 minutes after starting it, the bike shut off just like it did the day I had it towed. The coils have been switched to different cylinders but cylinders 2 and 3 are still the ones that are not firing. Does this narrow the problem down to the ignitor?

Or the pickups.

Since it's more intermittent, I think the pickups are a slightly higher possibility.

This can also be determined by swapping some wires around, if you want to know for sure.

In the little harness coming from the pickups, you have to swap the yellow and black wires, and swap the red and blue wires.
Then on the coils, swap the little green wire with the little black wire.
This makes the 1-4 pickup control the 2-3 circuit in the igniter, which is now wired to the 1-4 spark coil.
Also makes the 2-3 pickup control the 1-4 circuit in the igniter, which is now wired to the 2-3 spark coil.

If this moves the problem to 1-4, then the igniter is bad.
If the problem stays on 2-3, then the 2-3 pickup is bad. EDIT: or as Patton points out below, not ignition related.

This does not rule out a wiring problem, though. It only checks the pickups versus the igniter and assumes the wiring is all good, as in, not broken, frayed, dirty, etc., which can result in low voltage or bad signals.

If the igniter is not bad, then to confirm the pickups are the problem or not, more wire swapping can be done, along with flipping the rotor. If the pickups are not the problem, then you can move on to non-ignition possibilities with confidence.

Bad switches can do it too.
Steve

nickleo373 wrote: It's been a couple weeks since I've had problems with the bike but yesterday I turned it on and let it warm up in the driveway. About 2 or 3 minutes after starting it, the bike shut off just like it did the day I had it towed. The coils have been switched to different cylinders but cylinders 2 and 3 are still the ones that are not firing. Does this narrow the problem down to the ignitor?

If not already done, would perform the clear-tube test on carbs 2 and 3 to assure that the float bowl fuel level is within specs.
A too high fuel level -- even in an otherwise perfect carb - can result in an excessively rich mixture that sooner or later fuel-fouls the spark plug, which often causes spark failure in both plugs connected to the particular ignition coil.

Also, sometimes old hard worn-out spark plug wires can leak high tension voltage by shorting or partially shorting through to metal parts of the engine where the plug wire is touching or resting. Could be intermittent in cases where the plug wires are manipulated incident to various testing procedures, resulting in voltage leak in one position but no leak in another position. Failure of spark in one plug may cause spark failure in both plugs connected to the particular ignition coil.The solution is a set of brand new plug wires such as the excellent Dyna brand available from Z1 Enterprises which are inexpensive and come with the caps already built in, and won't leak voltage.

Good Fortune!