It's cool you're hauling the engine for the truck, in the truck the engine is for.
If you do decide to get rid of the PWM fan controller, be sure to wire the fans separately for dual fan control with the Edelbrock outputs, then you can offset the turn on temps so you aren't shocking the system turning them both on at once. Although I am forced to do that with my truck since it only has one fan control output, I still don't recommend it.
I would also ground the fans to the frame, so the ECU has a better ground path (directly to the battery) than the fans.