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If I was to get a remote start, I would probably opt for the one from Ford, assuming one is offered for your MY. If installed by a dealer, it would (should) be covered by a warranty and preserve the vehicle's warranty too. It would integrate right into the existing systems in the truck.
www.fordaccessoriesstore.com lists the parts available for '04-'07's. The kits aren't too high, but the installation may run as high as 4 hours.
Agreed. I had Ford install mine (alarm with remote start). It was covered under the normal warranty ... servicable by any Ford dealership. I've never had any problems ... works just fine. With the Ford setup, you won't need an extra key (or key chip guts) to place near the steering wheel. I believe most if not all other aftermarket alarm systems will require a bypass key ... which can be a small pain, etc. Past that, a lot of folks really seem to like the Viper systems.
Code Alarm and from what I have read it is the best aftermarket system for the fords. Here is a link where you can find them and they will even prep it for your truck as well as send detailed installation instructions including pictures. I also understand that they will spend what ever time necessary on the phone with you to resolve any problems you might have. Give them a call with any questions.