You want the top feeds, there are a ton more injector choices available for the top feed. All WRX's have top feed IIRC, the only cars w/ the side feed are the early STi's that needed them to clear the AVCS solenoids on the heads. I'm running top feeds on my car, but I'm using the Perrin fuel rails to make it clear the solenoids. If you can swing it, try to keep the '07 fuel rails and top feed injectors.
Going to TGV deletes (are they SP legal? do you care?) is probably going to save you a ton of work rather than trying to convert your ECU to handle the '07 actuator/sensor package. Alternatively, if you don't care about keeping the top-feed fuel system, just pull the entire intake manifold off the '04 motor and slap it on the '07. The manifold is identical, but now you've just ensured compatibility with the injectors, TGV's, TPS, and whatever else is attached to the intake manifold. However, I think that may violate the update/backdate rules for SP which is one of the cool things that you were getting out of the full engine swap.
I'd talk to Knucklesplitter about TGV deletes, he may be able to have you up and running in a jiffy if he's got parts in stock. Plus the weldless kit he sells for the '07 TGVs is only $52.
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