I'd recommend replacing the whole thing. While you can certainly purchase a couple of feet of coaxial cable, you'd need to re-solder the NMO mount, and depending on the type of mount, will require disassembly.
If you are mounting this on the side fender, or exposed on a headache rack, you need to be absolutely sure the underside is well sealed. Since the traditional NMO mount is designed to be installed through the sheet metal body of a vehicle, with the coax connection well protected inside the warm/dry vehicle, doing any other type of install puts it at risk. With fender mounts, the point where the coax is attached to the NMO mount will be exposed to water, road salts, oil, etc. and that can lead to early failure.
Of course the ideal location is on the vehicle roof, installed per directions. That means hole through the roof. Benefit is that it will work better and last longer.
But I understand not wanting to drill into your truck.
If you really have to go with the fender or headache rack mount, then go with one of these:
http://www.theantennafarm.com/catalog/larsen-nmokhfud-1123.html
The coaxial cable connection is better protected.
In addition, get a few inches of marine grade heat shrink tubing and slide it over the coax up to where the cable enters the mount. The marine grade heat shrink has an adhesive on the inside, when it's heated up, the glue melts and helps seal the connection. The tubing will shrink over the adhesive and help keep it protected.
Still, those mounts can leak. You'd really need to pay attention to protecting the mount, or you may end up going through all this again in a few years.
As for the headache rack, that can work, however it will not provide an adequate ground plane for most antennas. Although the side fender mount won't, either. This is where the roof top mount really helps.
You could go with a "no ground plane" antenna, a half wave design, and that will help it work a bit better with your mount, or the headache rack.