1. I've heard that K&N filters can ruin MAF sensors, so be careful when installing them. The oil used to clean the filters is said to be the culprit. Some enthusiasts like my father changed the intake manifold and throttle body to a much larger diameter one, to increase the amount of air taken in. He also used a much thicker gasket, something along the lines of giving the air intake plenums a longer travel so the torque increases too. Of course, using the stock throttle body will restrict flow so a much larger one, similar in size to the larger intake manifold, must be used so the amount of turbulence is minimized. You can always reroute the air to get colder outside air, as what my father did. He routed the air into the lower air dams, cut the fake side vents on the front SiR bumpers and installed the cone type filter there, out of sight to the common eye. However when it rains just be very careful not to get water there! If you want to retain the stock look and do without the fuss of rerouting, Morrissey's advice on using drop in K&N filters on the stock piping works too. It doesn't give a throatier sound, but that's the concept - sleeper ang dating.
2. The same principle is used for the exhaust manifold. Mandrell bends give the tubes a more consistent flow of air, thus minimizing the exhaust gas velocities. This allows the exhaust gases to exit faster than typical crush bent ones.
3. I think the same thing was said to my father about the size of the exhaust piping being 2" rather than a larger 2.5" but in the end it's best you hear and experience it for yourself. Your problem here is you need to find somebody who's willing to help you out on that
I too would stand and/or sit corrected if needed be this is just what I've learned from watching and observing my father modify his Civic.