Mike,
I'm not sure where you are mounting your antenna, but there are a few options for th ecoax. You can come through the firewall where your present antenna comes through. You may need to take a knife (razor) and make a slit. There are also rubber plugs around a lot of the wiring that comes through the firewall. You could also come up through one of the rubber plugs in the floor, just cut a small X in the rubber plug and push the coax through. I have never had a problem with grime or water ever coming up through one of those, but you could RTV it if it gives you a better piece of mind. If you are doing the MAGNETIC trick with the antenna you can run it down the channel behind one of the weather strips and into the compartment along and under the moulding. Really, it is your imagination as to how you want to run the coax.
Just be careful when you run it next to existing wires. You could end up with a problem of interference to the computer module. I always try to use double shielded coax and keep the coax away from the computer module. If I remember my math, the coax should be (468 divided by the frequency in MHZ times .5) John Kohl can help out there some more. that will give you a wave length and keep the SWR down. (Or any multiple thereof)
Good luck.
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