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It’s all the lights in rearI'm honestly not sure on Hannigans but I do know that the harness for the rear lighting on a CSC plugs into a CSC module under the seat. You may want to look under the seat and see if maybe some connection isn't fully seated. That would cause intermittent problems.
And just for clarification, is it all the brake lights and turn signals for both the trunk and the trike body? What about running lights? The reason I ask is that it could be a bad ground in one of the connectors that feeds the rear lighting. Take a look at this article and maybe check for this as well.
Honda GL1800 Rear Harness Grounds – Electrical Connection
electricalconnection.com
Yes I’ve checked all fuses an relaysHave you checked your fuses?
ThanksCheck that grey connector that is mentioned in the link I posted above. There are a couple grey connectors under the seat. It's supposed to be the large one you want to disconnect and inspect.