I had gone through a hole in the firewall towards the steering column and tried to completely avoid all electronics. Then I actually did exactly the same as you say and went out from the right side door (driver side) around the front and then onto the battery from top (and bottom) of the left fender to get to battery, the problem remained.
I know it sounds really weird and I do appreciate your input, it just did not work any other way. I have done searching on the internet and some other TJ owners have had similar problems with taking the power directly to the battery. It is working now, so I'll stop playing with it.
Thanks for taking the time to reply, TW