get the trans line presure tuned. For EX: With the 48mm TB, at 25% throttle, you had 100lbs torque. Now with the 52mm TB, at 25% throttle you have 125lbs torque.
Because the 52mm TB lets in more air at the same throttle position vs the 48mm(which is why it's more responcive), you might not have a high enough PSI for the trans, at the power per throttle %. I'd talk with Mr. Cobb, and Mr. Herter and se what they say.
See what I mean? Also, something I just thought about, because the TPS is seeing less throttle % for the amount of air, will the Air to Fuel Ratio be off?