Back from the dead

Hey it's been awhile since I've been up but I finnaly got tb back, if you remember it was the one with the multiple codes. The problem was the transmission was shot I took it to a shop and the guy actually let me watch him open it up and it was shot it was broken inside burnt etc. I got it back cost me an arm and a leg but I got it back. Ok now I want to know if someone could tell me what this might be, when I start it it feels a little rough meaning like it vibrates a little while I sit and wait till it warms up and as im driviving i feel on the gas pedal a little vibration nothing major but i feel it when i take off. I got the tires balanced air is good .what should I look at.
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