I'm not sure what part of the intake system would be considered secondary. Air box,Throttle body, Maf, any tears in the intake hoses? I would start there first. Vacuum leaks? With the 96 year onward being OBD II, I would think an OBD II scanner would also work.
1995 325I, tinted windows, K&N, debaffled air box, BMW style #104 wheels, Nighthawk low beams, smoked side markers, smoked corners, smoked taillights, M3 style heated mirrors, various interior bits, Bosal cat-back