Bizarre ignition problem on kz550

Alright, so...

I bought some new replacement coils from eBay. I put them on and went to go turn over the bike. The coil for cylinder 1-4 became very hot, while coil 2-3 stayed cool. Had to use starter fluid to get the bike to fire, and once it did, only 2-3 were firing.
so I thought, ok I must have fried cool 1-4, awesome. So I put the original coil for 1-4 back on. 

then the weirdest thing started happening, one cylinder 1 and 3 were firing. (Pipes on 1 and 3 were hot, while 2 and 4 were ice cold)

so I check spark, and I’m getting no spark on 1-4 but getting spark on 2-3. I understand than this means coil 1-4 is likely bad. But my question is... can anyone please explain what’s going on, and how 1 and 3 are the only ones firing, yet coil 1-4 is shot. 

I didn’t have time today to do a full run-down with a multimeter or look over any of the wiring.

I need the help so I appreciate any direction or advice. 

My first thought is that your plugs were incorrectly wired to the wrong cylinders.

Are these cheap/inexpensive made in china coils?  And did you install new spark plug wires? 

It may be that the coil getting hot is bad, possibly indicating an internal short. just guessing. 
Usually when coils are operating normally, they'll get warm but not hot. 
You could try swapping stuff around to see if the problem follows one or more of the components: coils, spark plugs, plug wires.

Martin raised a good point.  Check the coil resistance.

How did the bike run before?
Why are you changing the coils?

I did the swap method, and was getting no spark on just coil 1-4.

I contacted the seller and they’re sending me another coil. I ordered new leads as well and will be getting new plugs. I have the dyna s pickups on the bike. I’m replacing everything just for peace of mind; since everything on it was from 81’. 

it was running decently before doing the coil swap, but would not start without starting fluid. I figured replacing them would help remedy that problem; but I still need to size up the pilot jet.
 

Check voltage to the coil primary. Needs to be close to battery voltage. You need a good battery and it needs to be at full charge. Don’t touch the pilots till you get the bike running. If your running pod filters makes sure the rubber collar doesn’t block any of the small intake ports inside the intake mouth of the carburetor. If you have quality pods you need to install air corrector jet sold by Zed1015. With them you probably won’t need to change pilot jets. Before you can tune you need to make sure valve lash is correct. Timing is correct. The charging system is good. Hard start could be low primary voltage, carb float level, or choke enrichment not correct 

If you could start it with starting fluid, it may not be an ignition issue.



 

I'm going to be doing a valve adjustment soon. I still haven't gotten back to the garage to check out anything.

I have a gravity feed petcock on the tank, so the carbs will overflow if gas is left on. (I tried adjusting the floats multiple times to try and compensate for this, but all attempts have been fruitless.) but, when the bike is rolling down the road this isn't a problem; only when left idling on the kickstand.

I'll have to check out what you're talking about with this zed1015 guy you're mentioning. 

Pull your plugs.
What do they look like?

The overflowing of the carbs has me wondering if the engine was flooding before with the old coils.
You could have issues with your float valves.
Did you ever pull the plugs when it wouldn't start up?


Try something. I suggested this to someone else.

Cover half of your air filter with duct tape.
How does it run?

Take the duct tape off and create a small air leak by opening up the air filter housing.
Don't take the filter completely off as that will be to much air.
This will help narrow down where your problem is.
This is the concept.
www.motorcycleproject.com/text/the_60-40_rule.html
 

If one or more of the carbs is overflowing, then there is a really, really good chance that one or more of the float valves are not sealing. If that is the case, no amount of adjusting will solve the problem.

Use the clear tube method and try to set floats. If they level its adjustable then as mentioned it’s probably a float valve. Pull the float seat and needle and inspect them. Keep them as an assembly. If the tip of the float needle isn’t worn the seat and needle can be polished. Mother’s aluminum polish has just the right grit to work well.