There are differences in cam sensors across the model years and applications. The different types of cam sensors are NOT compatible with each other. In addtion the cam sensor, wiring harness, and PCM must match.
Don't mix/match parts from internally and externally balanced engines.
If injectors are a concern consider an injector cleaning/flow test service such as injectorrx.com.
My $$ is on something basic like ignition wiring. Are you POSITIVE that the correct spark plug wires go to the correct cylinders? Pictures?
Does any body know if Ford changed the firing order during the V6's lifetime?
2003 GT Convertible (sold & missed)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.