2005 Mercury Mountaineer hesitation at cruising speeds

I have a 2005 Mountaineer with awd and v6 4.0l engine. In the past 6 months it has begun to hesitate while at cruising speeds. When diving on the highway, the engine or transmission will start to hesitate or miss between 1000 and 2300 (approx.) Rpms. I had it into the dealer and they gave me a laundry list of things that needed done, most of which were listed in the manual at 60,000 miles. They did say that the computer showed misfires in the lower rpm range. They suggested I replace the spark plugs and wires. Which I had changed as well as change the fuel filter. Problem is nothing has changed. I personally think it has to do with the transmission. If it was doing this hesitation while driving in the rpm range, wouldn't it do the same thing while in PARK and just reving the engine if it was the spark plug suggestion.

I would appreciate any help that you may be able to offer to remdy this problem.

Thanks