1981 KZ550 Exhaust headers 3&4 are running colder than 1&2

Hi all, I bought my bike in February knowing nothing about riding or wrenching on motorcycles. It was in pieces, and with everyone here's help, both directly and indirectly, I've since rebuilt the wiring harness, replaced most of the faulty charging system, and replaced the carb holder boots. 

About a week ago I noticed that the two rightmost headers on the exhaust (3&4 if I'm not mistaken) are running much colder than the other two. I can spray water on the leftmost headers and it boils off right away. Water sprayed on 3&4 just runs down the header and drips to the ground. They're still getting warm, you definitely wouldn't want to touch them, but they're significantly cooler than the others. 

I waited until not to post as I was waiting on the new carb holder boots to show up, thinking maybe the vacuum leak (which was only present on carbs 3&4) could be the cause. That doesn't seem to have fixed it, so I was hoping someone with more knowledge and insight could help me get that figured out.

Thanks!
Mac

Did you sync your (clean?) carbs?

Make sure the plugs are wired correctly.  1 & 4 should go to the coil with the small black wire.  2 & 3 should go to the coil with the small green wire.

Usually the coil with the small black wire is on the right hand side of the bike, and the coil with the small green wire is on the left hand side of the bike, on the smaller inline-four bikes.  (The larger (900 and up) have the coils on opposite sides from the smaller fours.)

Water dripping down the pipes usually mean that cylinder is not firing at all or hardly at all.

Agree with a carb sync.  Also, adjust the valves if you haven't already done so.  Failing to adjust the valves will cause all kinds of various engine running problems, not to mention the engine will burn the valves and seats if they are not kept at the proper clearance.

Have you ever checked compression?

Is there a resource describing the method to sync them? I've looked around but haven't found anything.

How difficult is it to do the adjustment? 

Yes, the factory service manual.
You can follow the links in my signature to get several different manuals for the 550's.  I recommend downloading all of them.
Also, read the warning in my signature in case you decide to open the valve cover.

To do the sync properly and fully, you will want a precision tachometer. The bike's tach is not precise enough.
The sync is one of the last steps in tuning, though.  You need to set fuel levels and will want to check timing and valves if this bike is new to you.  

You can do a sync without all of that other stuff, but in my experience of synching 550's over the last 30 years, the sync would have to be way off in order to stop a cylinder from firing enough that water runs off the pipe.  If the bike ran fine before and the synch was not messed with, then synch is not likely the problem. 

A better way to troubleshoot the problem you are experiencing is to pull a plug wire off one of the dead cylinders and make sure it gets grounded.  You will need a small bolt or such zip-tied to the frame or head and place the plug wire on it.  Then start the bike and see if it runs worse.  If it runs the same then that cylinder is not firing.

Appreciate your help, Loudhvx. I went ahead and order a FSM from ebay. The Clymer manual just hasn't been cutting it. Is the valve adjustment something that can be done with the engine on the bike? Probably a stupid question. 

If the compression is good, the valve adjustment is close enough to start the bike.  Usually a valve adjustment problem on a 550 will show up when the engine is really hot from a highway run.  After coming to a stop it will stall since the valves will no longer seal enough to idle properly.  After a few minutes the valves will shrink enough to seal again and the bike will run normal.

Yes, you can do a valve adjustment in the frame.  You just remove the tank and coils and emissions equipment if it still exists. The FSM's I link to have the instructions.

I took a look at the plugs on the off chance that they were wired up incorrectly and they were. The coil with black wire is on the right, the coil with the green is on the left. But they were going to the wrong plugs. I switched them, and now it doesn't want to start. Does each wire have a specific plug it needs to go to? 

From the factory, the right coil had the black wire and connected to 1 & 4. 
Either plug wire of the coil can go to 1 or 4 and vice versa.

From the factory, the left coil had the green wire and connected to 2 & 3. 
Either plug wire of the coil can go to 2 or 3 and vice versa.

In order for the factory plug/coil wiring configuration to operate correctly, the advancer has to be assembled correctly.
That means, when the #1 and #4 pistons are near top dead center (TDC) the pointer on the ignition rotor should be pointing backward toward the pickup that has the black and blue wires.  During disassembly/reassembly, it is very easy (50% chance) of installing the rotor in the wrong direction.  The advancer has a logo "TEC" stamped into it.  When the rotor is facing the correct way, the point of the rotor should face toward the side of the advancer with the logo.

And, of course, the pickup wires and igniter wires must be wired correctly, color to color.