if you have your stock intake manifold leave your vtec point where it should be...4400. when you get a new IM your going to have to raise the vtec point up due to getting rid of the secondaries. Only way to truely find out where your vtec should be is by taking it to the dyno and watching where your torque and hp cross or meet eachother.

as you can see since i put the skunk2 IM i need to raise my vtec point to about 5200, where i start gaining my power back