One side runs, then the other!

[Greaser Greg]

What a can of worms!  Aftermarket harness, known working ignition assembly, 11 volts or more at brown wires to coils, two different sets of coils, plugs and wires all verified to run the left side.
Got the left side running after a full teardown and rebuild, switched coils wires and plugs from side to side. Same, then right side kicks in and left out, then back to left like someone flipped a switch.  Left side was running, messed with coils then right side ran, then switched to left again by itself.    No obvious shorts or bad connections so far.  Haven't cut into the harness sheath for an inspection yet. Everything looks good in the bucket, and all the lights and horn work fine.  Reg wires came out of plug so waiting for battery to charge then back at it with tester. 
Lemme make sure I got this right:  Juice comes from the brown wires to the black (emgo) or brown (oem) wires on coils. Leaves the coils through the yellow (emgo) to orange and grey wires, orange to the left cyl, grey to right. Points open, field collapses, juice to plug and ground.  Bang! The condenser absorbs the electrical shockwave to prevent arcing across points.   Right?
Must be a short somewhere in the harness between the ignition plate and coils, no?   

[Dvsrd]

11 volts at coil positive terminal is really low. It should be very close to battery voltage. A healthy battery has 12.6 V. 12.0 V is what you measure on a totally discharged battery!
With a running engine, a healthy battery and a good charging system, battery voltage should be close to 14.5 volts.
Even at that battery voltage, the stock RD ignition system could be described as marginal. Now, the difference between 11 V and 14.5 V will not make it any better.

To troubleshoot your problem properly, first make sure your battery is fully charged. That means reading MINIMUM
12.5 V after sitting disconnected from the charger for at least half an hour. Do not connect the positive battery terminal to the harness. Instead try a temporary direct wire from the battery + to the coils, with a 10A fuse just in case. This will bypass any resistance in the wiring loom and switches. Now you can check if your ignition system does what is supposed to do, make a good strong spark. If you decide to start the bike with this wire hooked up, be prepared to unplug or disconnect quickly, should you need to stop the engine. If this quick test shows that the ignition system works, you need to eliminate any resistance in the current path to the coils. That is wires, connectors, ignition switch, kill switch  more wires and connectors. And also identify any short or other issue in the harness that may be drawing a current and pulling the voltage down

If I still had the points ignition on my RD, or any battery powered electronic ignition for that matter (VS/Dyna, Newtronics, etc) , I would definitely use a direct power supply from the battery, via a 10A fuse and a common relay, to the coils (and "black box" if applicable) And just use the original brown supply wire to control the relay. I have done this on my XS650..

[AAAltered]

Wiring issues aside, as dvsrd stated good voltage is a must to run.  When I had a failing charging system (bad brushes, glazed rotor etc) I could run on a charged battery but it would die as the battery bled off, dying at somewhere like 10.8v.

[m in sc]

yup. might be charging issue. emgo round coils IMHO are garbage, id run the stock style replacements ,02

[Greaser Greg]

I'll try all these great suggestions, thanks.
Now it's stuck running on the right side only. lol
Why might I get continuity from the points wires to ground even when points are open, with or without condenser connected and cardboard between other points? One side does it, the other not.
I unplugged the connector from the ignition and cleaned and tested it. All the beeping from meter stopped when I moved the kickstarter so that elimnates a short from there down, right?

[Dvsrd]

Sounds like you may have a chafed wire or other short to ground between coils and points. What about the 4 pin connector for points and field current?

[Greaser Greg]

I just cleaned and tested that. All the wires isolate at that point.  It's some kind of aftermarket harness that was installed by p.o., disconnected and reinsalled by me, so, who knows what's going on in there.  Everything else works.  I did replace a melted connecter on the a/c outlet

Sounds like you may have a chafed wire or other short to ground between coils and points. What about the 4 pin connector for points and field current?

[Dvsrd]

That 3 pin/ 3 phase AC connector is a well known problem. Another example of marginal OEM designs on the RD. I would replace that one with a sealed AMP connector, or just a solder splice+ heat shrink.

[Greaser Greg]

I'm thinking there is other hidden damage since I get a completed circuit between the points leads and ground even when points are open.

[Dvsrd]

I'm thinking there is other hidden damage since I get a completed circuit between the points leads and ground even when points are open.

Then just bypass the harness with 2 more temporary wires, to verify this. 0.75 sq mm is sufficient between coils and points.

[Dvsrd]

I just came to think about another possible cause to erratic/ intermittent ignition issues. Worn crankshaft main bearings.
With points ignition, any slack or play in the main bearings will make the breaker cam move around a bit. Depending on how severe this movement is, and what gap settings the points have, it will make timing fluctuate badly, or stop sparking altogether.
(Even with brand new bearings, this will be happening, to a minor degree. The geometry of the whole alternator/points cam/crankshaft is not exactly ideal. External flywheel trigger, like on the Vape/ Powerdynamo has a lot better geometry for precise triggering of the ignition. Closer to the main bearing, as well as on a much larger radius)

[m in sc]

i firmly believe this is just classic low voltage symptom.

[Dvsrd]

i firmly believe this is just classic low voltage symptom.

I agree that low voltage is the most likely cause of this. Either due to a bad battery and charging circuit, or a lot of resistance in connectors, loom and switches.

The issue with worn main bearing(s) is something I encountered on my own 350A, before I bought it. I was working on it for my cousin who bought it new in 75.
New points and a new capacitor (condenser) Set timing with a dial gauge and a test lamp. And it was running like a dog. Check and re-set timing many times over. Same result. Finally tried with my timing light (strobe light), and I could see how the timing was jumping all over the place. After a quick crank overhaul, timing was as good as it could be. So at least for that bike, the main bearing was the issue.

Still, I got a Powerdynamo/ Vape CDI for it, as soon as I bought it. Pretty much the best mod available for any old points ignition bike IMHO.

[AAAltered]

The charging system isnt hard to troubleshoot.  There is an 18 step checkout in the R5 factory manual.

Im quite sure the exact steps and measurements are done on an RD350.

http://www.2strokeworld.net/forum/index.php?topic=332.0

Greg it looks like you were visiting that link back in 2019...

[Greaser Greg]

Thanks for all the suggestions! 

The combination of low voltage and different size pins in connectors seems to have  been the cause.  Reg/rec combo plug uses a thinner blade than stock, so when tested seems fine, but the contact is to weak for running conditions.  Pinched the slots with pliers til it was a tight insertion ( ) with the blades. 

Disconnected the neutral light to eliminate some draw. Things improved a lot after that move.  It was blinking.  May have been shorting in the tach housing. The rubber insulator cracked when I removed it and may have already been split.

The main switch harness has been messed with, too.  Looks and feels like some repair was done in the past; tape wrapped around some conspicuous bulges both below the switch and at the plug to main harness.  Guess I oughta dissect and explore in there since downstream voltage is around 11.4 -11.7 ish.
Then on to jetting! 

Thanks for sharing your wisdom and encouragement.