I have a 2002 F250/V10- 4:30 rear- Truck has been very good to me- has about 120,000 miles on her. I tow a 5th wheel that weighs about 8,000 pounds. After years of towing her with no issues- this week...
I have to ask, why did you put in the K&N? Every reputable "improvement" shop recommends against using the K&N. The reason is the K&N allows larger dirt particles into the engine, which is not a good thing.
You have the improved crank (vrs the introductory engine) 2 valve engine.
There is always an engine tuner (chip), you could contact 5-star Tuning and see what they recommend.