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Except for maybe a vacuum hose hookup, or possibly a kick down linkage, your intake manifold doesn't have a great deal to do with your tranny. Tell us what tranny you have.
if it is a factory auto, it is a C4...better question is what year....in all actuality, for most stangs, the Performer puts everything back into the stock location. The biggest issue is if it is an early 65....
When I put in a new intake Al Edelbrock manifold into a 67 289. the only extra part I needed related to the trany was because also I put in a new carb. You can always call the Edelbrock tech support line.