JB4 will work fine regardless of the air intake/exhaust set up.
Map 5 will autotune, or you can just set it to Map 1 which is the most conservative map.
My understanding is that most if not all air intakes makes little or no difference to BHP, and actually the stock box is pretty good. A quick search in the US forums will show up dyno plots of the stock box vs the dual cone intakes...essentially not that much difference, well not compared to what the JB4 tune does to the engine output anyways