I have asked Rich at FASTMANefi a few times, and he splits the system and puts injectors above and below. He says he wouldn't do it any other way. The uppers seem to be to keep the blower cool, and the lower port injectors keep the engine happy and in its correct A/F.. The older blower intakes do not lend themselves well to this, so the Indy intake is one of the few choices you have....
