My ED30 was stage 1ed for ages before I put a downpipe and S3 intercooler on. Standard intake on mine.
Neither made a significant change to performance but I need to get the map tweaked for the reduced back pressure really. My 'stage 1' map needed the Loba and a clutch, so it already has the fuelling headroom for tweaks.
Most tuners already delay N75 intervention early in the rev range on K04s to get it spooling, so there won't be much of change 'under the curve' with stage 2. The difference will be in the meat of boost, 3000-5500rpm, which will need some N75 tweakage for your turbo back. If you put your exhaust and intake on now, you will probably find the boost ramps up at 3000 too fast for the current N75 map to deal with, and it the ECU will pull it back. But you will also find that after 50 miles or so, it will adapt and smooth it off.
In any case, fuel is proportional to air mass, so it will self adjust......if your standard pump can keep up. Personally, to avoid any danger of lean running, I would fit your bits a week or so before the mapping date, then drive it around with moderate throttle to adapt. Avoid planting your foot right down and you should be OK.