The struggle to get air is usually a sound made by the Idle Air Controller, as it is letting some air through. This is normally a noise blocked out by the stock air box. Many people with after market intakes deal with this noise, and it is prevelant especially on cold mornings.
Usually, I check the cat convertor by disconnecting the downpipe and rocking the block. If it is clogged, the problem will go away. Be careful if you do it, as you will be running with open exhaust, and the noise is usually quite horrific.