My 1999 F-350 lariat 4X4 7

My 1999 f-350 lariat 4x4 7.3 has a shuddering problem when you get into overdrive and gradually accelerate. One friend said to change the filter and flush the transmission fluid so I did but it did not help the situation. Another friend stated that the truck might have had a chip on it before therefore the transmission would not shift right with out the power chip on the truck if the previous owner done some modifacations to the transmission. I also done the test of putting the truck in drive and holding the brake and the truck gradually started to shudder. I have just rebuilt the turbo also. The truck came with a turbo rebuild kit. Where do you think the shudder is coming from?