Rough Engine after 30 Minutes

1979 KZ650B all stock. have not ridden much this year. did my normal maintenance routine this summer, had a couple short rides, no issues.
last month, about 20 miles/ 30 minutes into a longer ride, engine gradually became very rough, low power for what seemed to be intermittent ignition, had to nurse it home, stalling and rough the whole way.
I suspected the points/condensers, it had been awhile since replacing. but i wasn't sure if it wasn't also fuel delivery / petcock related.... I have vacuum type, and it was leaking.
first, the petcock: I pulled and rebuilt, the tiny check valve was stuck.  but if it wasn't shutting off fuel, that wouldn't explain the rough engine. so, I eliminated fuel delivery, or at least the petcock, as the culprit (it still leaks a bit which is really annoying - it never used to - i think the check valve is damaged).
points/condensers: points were pitted. the condensers were older KZ ones I had found on ebay, testing with multimeter, they seemed OK, but I replaced both points and condensers with a spare set I purchased from from Z1. set dwell, timing, etc, and the bike came back to life, starting nearly immediately, smooth and lovely. took some short rides, all seemed well, better than ever. bike sat for a coupe weeks...
yesterday, about 20 miles/ 30 minutes into a longer ride, same issue as last month. so bad, got to 1/2 mile from home and could not get the bike to stay running, had to push it home.
my current guess is a temperature related issue, something ignition related is failing at higher temps, coil malfunction perhaps? or the plugs? they are not that old, and tested fine.. I am going to check them again, but if they were bad, wouldn't they be bad all the time? not just when hot?
input welcome / appreciated.

Welcome to KZRider 
please make a intro post in new members  
Dave

That petcock may be the problem. The vacuum line from the carb may be sucking fuel from the leaky petcock into the carb causing the mixture to be too rich to fire reliably. 
When rebuilding a petcock, it is a really good idea to carefully inspect the surface that the little oring seals against. If it is badly pitted, the petcock is junk. If it is not badly pitted, it should be carefully polished to a fine finish to provide the best seal possible. I also polish the face of the lever where it seals against the large rubber seal.

If you think it's electrical you will need to take voltage readings when it's faulting. If you have corroded connections this causes a resistance, resistance causes heat in the connection which then further increases the resistance until you reach a point where not enough current flows. Once you switch it off and there is no current flowing the connector will cool down and the resistance will decrease again. Once you re-start the whole cycle starts again.

first, the petcock: I pulled and rebuilt, the tiny check valve was stuck. 

Rebuilt? So, you installed new rubber parts? If so, what brand.
I would try running the motorcycle on PRI; you may need to cap the vacuum port.
This is what I did one time when the diaphragm failed & was spewing fuel.

When was the last time you checked your valve clearances? 

Thank you for the replies! Answering questions:

When was the last time you checked your valve clearances?  I set them last summer, no more than a couple hundred miles since then.

Rebuilt? So, you installed new rubber parts? Yes, I had a "new" disk and o-rings from a rebuild kit I bought from Z1 some time ago. The diaphragm and the plate in the "sandwich" are NOS Kawasaki. I had first rebuilt diaphragm from the aforementioned kit, but after trying that, and the problem persisted, I noticed some tiny cracks in the plate, so I got the NOS assembly and installed that. I also spent some getting the vacuum port check valve to free up with carb cleaner, but I worry I might of damaged it in the process.

Following up on TexasKZ's reply, I noticed fuel leaking from the outlet side as well as the vacuum side (see pics). The diaphragm and plate are new... how is fuel getting over to the vacuum side? I then pulled the tank so I could remove the petcock and inspect. I When draining the tank, I switched from PR to ON, and the flow stopped.  With petcock off, I pulled the drain plug, and applied suction to the vacuum port, and could see the plug move in and out. Disassembling, I noted the surface the diaphragm o-ring to be sound, and the check valve rattled around freely. Still, something's not right with the petcock, and I want to solve this issue before moving on to any possible electrical issues.





 

Since last post,
- Installed new petcock, confirmed operating properly, but same performance issue after short ride (but thankfully no more petcock leaks - one issue solved ).
- Installed new condenser set (DAIICHI aftermarket), bike started right up, sounded "right" but had quite a bit of arcing on points (they are not that old - a set bought from Z1).
- cleaned up older OEM set of points, installed, set dwell, timing within acceptable range, but bike runs rough, sluggish with throttle, still some arcing.
- went back to newer set of points mentioned above, but bike still sluggish, although points did not seem to be arcing as much anymore.
- started investigating voltages per posts here... noted voltage at coils (with leads attached) about 9.2.
- 2 rounds of cleaning the kill and the ignition switches got me 12.2v at the + leads to coils (battery 12.5), but as soon as I connect them, the voltage at + coil terminal drops to 11.2. nice improvement, but why the drop when connecting?
- strange (to me) that the bike ran pretty well before all this when I was unaware of the low voltage at coils.
- checked spark, all 4 look pretty good on tester. coil resistances are good.
- checked grounding on points - 0v
- pretty stumped at the moment. was thinking of a carb synch, but mainly b/c I'm not sure were else to look...
Input appreciated!


 

Are the original coils still installed?  Maybe check to see if they're getting hot after riding >> they should get warm, not hot. 
I was having a problem with intermittent firing on #1 & #2; both coils tested fine and the spark looked good to me; but after doing just about everything else from a fuel tank cleaning & new petcock kit to rebuilding the carburetors and checking the wiring, ignition, and valve clearance, the problem turned out to be the ignition coils. Mine were getting very hot to the touch.  you may have to press firmly with your fingers to feel the hot heat. my neighbor had the same motorcycle, so I was able to compare. not really necessary, but it was handy.

Could also be a plugged fuel tank vent.

Thanks much for the replies.

martin_csr re: coils, both replaced, with EMGO aftermarket, probably 8 years years ago, not a ton of miles on them. i haven't checked how hot they get, but will.
good news: i double checked my voltages, and i'm getting 12.2 at the coils. the bike starts almost instantly now.

TexasKZ re: plugged fuel tank vent: are you referring to the vents on the carbs? let me know where i should look.

not so good news: the new cheep-o petcock is leaking on the fuel outlet... getting a little puddle of gas under the bike while it's sitting.
 

The gas cap on the tank has a vent in it that lets air in as the fuel goes out. If the vent is clogged, the fuel going out of the tank into the carbs as you drive will create a vacuum in the tank that will nearly stop the flow of fuel.