Before you consider any upgrades, visit a reputable mechanic and make sure your vtec is connected and functioning correctly. Have them check to ensure nothing else has been missed, and do any regular maintenance it still needs. Consider having them perform a full fuel system cleaning as they can make a huge difference. Once all thats done, drive the car around for a while so you get a good feel of that engine. You have yet to drive your engine in tip-top condition so you really dont know how it performs yet. Once you do, THEN begin to consider upgrade options.
If i were you, I'd "upgrade" back to a stock air intake box and drop in a K&N air filter. Keep the tube if in the future you really upgrade the engine. if the filter is even a decent brand.