Check with Xtreme Mustang Performance in Aliso Viejo. The do some sick work. I am not sure how extensively the deal with transmission and I they have built numerous Stangs with serious power. Eric is this resident master wrencher he prepped 11 cars for the 2005 SEMA Show last month.
As far a regular transmisison shops the only recommendation I have would be Mission Viejo Transmisison I have had good experience with them on one of my cars they rebuild an auto and added an aftermarket torque converter for me.
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