2006 Ford F-150 spark plug change or injectors

I have some type of hesitation in my engine. Originally the dealership told me it was the transmisson. They called it a 3rd gear shudder. The only time this would happen is when I was on an incline, I can get it to duplicate it by keeping the rpm's at the line right before the 3. Once the incline levels out and the engine shifts into 3rd gear, it hessitates, like a misfire. They replaced the transmission and it is still doing it. I took the service rep for a test drive again and it is doing it worse since the transmission replacement. He told me the plugs are misfiring. The problem I have with that is first it was a dirty fuel filter. Then another dealership told me it was the transmission. Now after having both replaced they are saying the plugs, which is what I have said from the begining. My problem is the coils may need to be replaced and will not be covered under warrnenty because it is a maintanence item. How do I know, or will I ever know if it is the plugs/coils versus the injectors? I have been doing research on the internet that has said that the 05 F15o's had a bad batch if injectors. My vehicle was manufactured in October of 05, so technically it is an 06. Do you suggest I get the injectors tested before paying almost $1000.00 for a plug/coil replacement, only for that not to be the problem. This has been a horrendous experience considering I just bought the vehicle 3 months ago. Any help or advice would be greatly appreciated.