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I think you will see some improvement when you run that 87 out and install the 91 performance tune. My 06 acted the same way until I installed the 91 tune and that made a world of difference.
I haven't messed with the trans options yet but just turning off MDS and the 91 tune made the SC worth the price for me. My magnaflow doesn't sound like a fart can when MDS is on and having hand calculated many tanks of gas both pre and post MDS I can honestly say my gas milage is slightly better now than stock.