In a 2005 4.4 you should have the ZF 6hp26 transmission, i'm not currently aware of any problems regarding that transmission. What kind of mileage do you have on it already? Could possibly be a pressure regulator, I would think it might be a bit early for a failing clutch pack.

However I think it may be more engine related if you are experiencing hesitation etc. The above issue would be more attributed with slipping or issue with gear engagement. So do you possibly have a misfire, Vacuum Leak, etc?