Firstly, you are right, here is all things civic (of the M variety) Secondly, can you fill in your profile properly please mate ..
And onto your problem .. As you will find, there are multiple threads on the forum regarding the "two stage vtec", "two step" whatever or however you want to call it .. The vtec is engaged at 4500 rpm - this is the actual engine changing its characteristics (cam duration) and this is why you can still hear it .. The second stage, is the butterflies on the inlet manifold opening to 100% at 5800rpm ..
The reason this sounds has probably gone is the noise of the exhaust ! lol .. Get a decent induction kit on there and it'll probably return.. Having said that, I have a 4-1 straight through 2.25" system and not a fancy intake (just 3" piping and cone) and I still hear mine without any issues ..
And lastly, no, you don't need to worry about any sensor issues.. The standard cat never had one .. Just need to find a friendly MOT'er..
Also, might be worth resetting your ECU after this work .. Allow it to calibrate itself again .. If you don't know how, have a search, there are numerous threads ..