Check your Cat Converter and o2 sensors too if its still happening. Something very simillar happened to me like that and I was so paranoid that it was the transmission and I was screwed in having to buy a new one, instead it was just a clogged catalytic converter 
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2001 GLS 3.4L Coupe "Black Mamba"
Mods: K&N Cold Air Intake, 8000k H.I.D. Low Beam, 3000k H.I.D. Fog Lights.
Wants: SLP Exhaust, Ported UIM & LIM, 65mm TB, Lowering Springs, Rims, Black Interior.
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