Hoobie7,
I've been thinking about your problem for about a week, and I have some ideas. Let's find the solution.
The specs on your lights are 11 to 16 volts operating range with less than 1 amp current consumption. The flickering must be caused by low voltage. The front lights don't flicker with the engine running, so no low voltage problem at that end of the bike. The wiring difference between the front of the bike and the back is the ground location. The schematic I have for your bike is from the Clymer manual, and it shows the front lights ground near the lights, probably in the headlight bucket (though the schematic does not show a ground wire from the bucket to the frame). The rear lights ground at the main ground point somewhere on the frame. On you bike, it appears to be on the left side of the top frame tube at the coil mount, that group of brown wires. Clean this ground lug and the coil bracket thoroughly. If the ground lug crimp looks badly corroded, cut it off, restrip the ground wires and crimp on a new lug. I would recommend adding another ground wire from this ground point directly to the negative terminal on the battery. Now try the lights with the engine running.
As an additional suggestion, get rid of all those 'scotch lock' splices. Those are the blue in-line splices I see in the headlight bucket and the taillight housing. They will always develop corrosion problems and cause unreliable connections with time and exposure to the elements. Solder or crimp butt splices with heat shrink or liquid electrical tape as necessary is always a better, longer life solution.
Let me know how this goes. We can fix this.

Andy
ABC #15601

As an additional suggestion, get rid of all those 'scotch lock' splices. Those are the blue in-line splices I see in the headlight bucket and the taillight housing. They will always develop corrosion problems and cause unreliable connections with time and exposure to the elements. Solder or crimp butt splices with heat shrink

+1 on the in-line splices.... Additionally, get rid of the wire nuts seen in the tail lamp housing.

You want to use the same high quality level of wiring termination as seen under the hood of a new car. Everything else goes intermittent in 6 months on a motorcycle, where it's exposed to mud, wind-driven water, ice, hot oil, fuels, etc. It's an extremely rough environment.

Also looked through your photo album. Very interesting.

The "Max Protection/ Max Power" spark plug cables you have shown on your bike may be the incorrect cables. The only cables I could find listed on their web site are "suppression" type spark plug wires for cars, and those are not correct. You should be using metallic core wires with 5,000 Ω plug caps.

That's funny as I've spent the last week or two ignoring the problem out of frustration. 😉 However your posts have inspired me and I am back on the case. As for the vampire splices(scotch lock), those were one of the first things I got rid of after I bought the bike, I hate those things. As for the wire nuts, those are gone too. All of the taillight stuff got cut off and I got myself a Weather Pack kit and terminated it properly. There are pics of that effort in the album that are hopefully visible.

A bit of history on the bike and myself. This is my first motorcycle and I bought the bike off Craiglist in a non-running state from a guy two hours away. Probably not the best idea for a first bike but it's what I wanted. The guy I bought it from only had it a few months and had a couple other bikes in the garage so I think he was done trying to make it work. I think the owner before him had put on a full fairing and hard bags of some type, that would explain all the wire splicing. To get it running last year I mostly just had to plug wires in to their proper places. The key tumbler was wired wrong so it wouldn't turn on, the coils were wired wrong so it was running on one cylinder. I found several of the color coded wires were simply plugged into the wrong color on the board. Once I got that all sorted the bike ran pretty well and I rode it all last summer. It was not without it's issues though. It had a headlight relay go bad, it left me stranded once when it died and would not restart, it was blowing fuses when I used the turn signal due to a frayed wire. Needless to say I have worked through some electrical issues with it.

As for this issue I've tried may things:
- I thought it might be EMI so I wrapped the plug wires in tin foil
- I replaced the turn signal relay since I have LEDs so I unplugged it entirely to isolate the issue
- Since they seem to flicker with the engine PRM I unplugged the voltage regulator to try and isolate the alternator
- I unplugged my battery tender thinking it might be causing an issue
- I plugged in other LED lights to see if they did the same thing, they don't
- I thought it may be a short in the rear light wire loom so I ran jumper wires all the way to the back

So for my next steps I think I will fix that ground bundle as it is frayed almost all the way through one wire. Then..... I don't know.

Ya, I also did not like the mismatched plug wires. I replaced them with these NGK 1k Ohm wires.
The application table says they should be right but I will look into that as well. Thanks for the tip!

Just a warning. If that's the "NGK Application Table" you are referring to, then it is riddled with errors on older vehicles.

I looked at the Application Table tab on that page. The similar 5k ohm wires did not list R75, only R65 and R100. However I have also not been able to find a corroborating source yet.

If that's the "NGK Application Table" you are referring to....

My bad. It is NOT the NGK table you are looking at, but rather the EuroMotoElectrics table. I didn't see the link in the first post.