I purchased a used F350 from that an auction and it did not have the remotes. It has an alarm system that was an add on from Ford, I think it is an System 4 or 6. There is a bypass/reset switch under the dash and a red led on the dash that flashes. Can anyone advise on how to get the remote system into program mode?
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I've never heard of a System 4 or 6 alarm before but basically you need to find out exactly what model it is and then go from there. Check with the manufacturer and see if you can get replacement remotes and what the procedure is for making it learn new remotes. Also this is the Interior Care forum, you'd have better luck under the Aftermarket/Other Aftermarket section.

 

I would suggest trying to locate a serial number of some sort and going from there.