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So... I installed a Cobra 29 WX NW ST in my 2004 F-250 a few weeks ago. I ran power for the CB directly to the battery using the factory pass-through wires that run through the firewall.
My antenna is a magnetic roof mount from radio shack (I know probably not the best, but it'll do for now). I ran the coax cable from the antenna through the top of the 3rd brake, across the ceiling above the headliner, down the driver side pillar, and under the dash to the back of the CB.
Overall, it's a pretty clean install... I like it. But... I am getting interference when I turn my AC on. The higher up I turn the AC, the worse it gets.
Also, right now my SWR is 2.0 on channels 1, 19, and 40. I do plan on getting it tuned in better at my local CB shop.
Just a thought here....I am no electronics expert, but have you tried running the power directly to the battery by not using the passthrough wires? The passthrough wires are surrounded by many other vehicle electronics and could be causing interference.
When I installed my CB I ran dedicated wires directly to the battery as far away as possible from any major cable runs in the truck. Made the install a lot better and reduced feedback to near zero. (I know it is not the easiest way of doing things, but this was the easiest way to get the audio quality I was after).(Same goes for the coax cable as well)
Your issue most likely stems from the too long antenna run. Even a cheap Radio Shack antenna is limited by the quality, length and proximity of its lead to the CB. Its doing its job in picking up airwaves but too many are unwanted or interference.
Find a shorter run for that cable and most of this should disappear.
Your power source is almost always going to be your problem. Use shielded wire (such as antenna cable) to run directly to the battery preferably with as short a run as possible and NOT in parallel with other electric wires. Also make sure antenna cable is not running parallel to any electric wires, either...
That's pretty much how to do it, that being the same guide I used to do mine. 9 times out of ten, it'll be a problem with the coax or power source that is causing interference. I just drilled a hole in my firewall and ran my cable straight to the battery and I haven't had any real problems with it. Like many others have said, isolation of your coax from all other wires in the truck will help the quality tremendously, and reduce the interference. Not sure if this helps at all, but this has been what I've discovered during my CB installs.
I run low loss mini-8X coax from my (1985)Cobra 148GTL to the driver's side tow mirror where I have a mirror mount fiberglas K40 whip, 12vdc I have coming off the hot power point 20amp fuse on the fuse panel.