Issue fixed! I had done a tune-up about 3k miles ago except for the fuel filter. Finally changed that and the hesitation is gone now. I also replaced a leaking fuel line between the filter and throttle body at the same time. The hesitation was there way before the leak started, so not sure if...
I know this is an old thread, but was wondering if OP figured out the solution because I'm having basically the same issue. After initial start up when engine is cold or after sitting for a few hours, truck will hesitate and bog down with the initial acceleration, then runs fine afterwards.