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As long as the CB antenna is cut to the same wavelength as OEM and offers the same impedance (should be stated somewhere on the antenna you removed) you should be good for plug-n-play.
In my electronics days, I found antennae were rarely the root cause of reception/propagation problems (unless they were physically damaged). Most of the time signal loss was due to corroded coaxial cable connections, broken shield connections, bad connectors, shorted center conductors (always assuming the antenna pre-amplifiers in your radio haven't gone south).
If you have an old car antenna available, you might consider hooking your am/fm radio lead up to it to see if there's a marked difference; if not, then it's most likely one of the factors I mentioned above.
In any case, once you've disconnected/removed the antennae from your bike, you might want to inspect and clean all your connections and the antennae bases. A combination of emery paper and tuner cleaner or rubbing alcohol will generally do the trick.
I'm betting that one or both of your antenna connectors/connections is dirty/loose/damaged.
Good luck:leprechaun: