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Right out of the box will a apex power fc start the engine and run like a stock ecu. I have the controller, Or should I start the new engine on the stock ecu, And then break it it, And go get it tuned with the power fc.
Depends on the mods. If it is a basically stock FD, which it must be as you are talking about starting it on the stock ECU, you should not have any problems firing it up on the base map provided be Apexi.