If the earlier 3rd gen trucks use the same trailer wiring through the TIPM like the '06+ trucks this is a logical place to start considering your problem didn't arise until hooking up your new trailer. When the TIPM failed on my '06 I would only get 3v to the right brake/turn on the trailer circuit, however lights on the truck all still worked fine.
Have you checked the voltage on the trailer circuit on your truck to see if the problem is present there as well?