I currently have a Wilson 1000 magnet mount stuck on the roof, but I am going to go with a permenant mount Wilson 1000 soon. Wilson or K40 are good antennas...either one.
I've had several different kinds of antennas mounted in the bed, and they were OK, but none that really stood out.
Remember this, the antenna is the most important part of the set up...a quality antenna, with good coax, and properly tuned will make the cheapest radio work better than a high dollar radio on a crap antenna.
As for radio, in my Duty I've got a Cobra 18 whatever it is...the smaller one that they had at Walmart. I've got an old Midland in my YJ, and I've got a Cobra 29LTD that was in my old buggy. I like the 29LTD very well, and would rather have it one in my Duty, but the size was a problem...with the console, bucket seats, and two shifters on the floor, the only place left for a radio was over the little trash bag hook thing.