I would not lower the vtec point with just an intake. Honda tuned vtec to kick in at the optimal moment, with just an intake i dont think there is much reason to change it unless you decide to do more extreme tuning.
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lowering vtec wont make you loose power... you just may not gain anything and you will loose fuel economy...
vafcII is basically a piggy back unit, all piggy back ecu's and controllers interupt the signal from an engine sensor and then send a slightly different signal to the stock ecu, this will make the car run differently :D its basically the same princible as those resistors u put inline on ur commobore intake temp sensor so the engine runs as if its cold and you get more power, except it goes a lil bit more complex than that...
as others have said (i can confirm from personnel experience) the honda ecu is very quick learner... only took 2days from my rbc swap for the ecu to completely re-map its idle and running setings... not sure how the whole vafc re-learning goes, but the settings probably wouldnt stay all to long :(