You are making this way to complicated.
I would go with the wire behind the glove box route. Trying to hook a connector to the battery is a pain.
You should not have engine noise through the CB but if you do go to a CB Shop or Radio Shack and by a inline filter for the positive side wire from the CB. That will take care of the noise problem. And by all means make sure you wire a fuse into that positive wire also if there is not already one. 20 amp should do it.
Also get a meter and make sure your CB is matched to the antenna,Radio Shack Also, cause without that your noise will be the least of your worry's.
Use good Coax, not cheap stuff if you want to get out, preferably 18' in length. If you can't find a way to wrap that around use 9' but nothing shorter.
Get a good antenna also, Tunable Firestik will work on a Jeep but a Wilson would be better but may not look right.
Hope this helps