EGR and PULSE AIR are TWO ENTIRELY DIFFERENT SYSTEMS, and use TWO ENTIRELY DIFFERENT SET OF PIPES.
EGR is for performance as it reduces the combustion chamber temperatures to reduce emmisions of NOX, a gas that is emitted when certain temperatures are reached.
The EGR does no harm to performance at all as it turns off when at full throttle anyway, IF GOING RIGHT.
If having trouble just take off as it clears a lot of piping out of the way, but will not harm performance leaving on.
Make sure that you leave the EXHAUST GAS PRESSURE DIFFERENTIAL SENSOR connected(electrically) though other wise it will go into LOS, on SOME FORDS.
tabetha