A HBP w/ S4 manifolds and stock ecu? What's the point? If you have the S5 manifolds, why don't you want to use them? Also... I highly recommend an aftermarket ECU or at least a retuned stock one. The stock ECU doesn't perform well with a BP motor.
Of course, you can run the engine and putt around until you get that ECU squared away, but it's kinda like having a super model girlfriend who's still "saving herself"....
Good luck with the build.