I had an AEM CAI from a '95 GS-R in my '92 CX. It touched the overflow bottle for the radiator, didn't hurt anything, but it did touch (I was going to relocate the bottle, but never did). My '92 CX also didn't have a threaded hole in the top of the frame rail to install AEM's mount (A GS-R would have) so I just let it sit on top of the frame rail. This caused it to rub against the front tranny mount and when I pulled it off a year or so later it had started to rub a hole. I hadn't failed and actually opened yet, but it was rubbing. I covered the spot in duct tape and later too the mount off and grinded the corner that was rubbing with a bench grinder and didn't have any other issues. I would assume the issues would be the same with an EK chassis ('96-'00 Civic). The skunk2 manifold relocates the TB to the normal B-series location and you can use the CAI for a '99-'00 SI. The factory dual plenum B18C1 manifold puts the TB a little lower than normal so you have to use a GS-R CAI or probably any under the hood style intake (most of those can simply be adusted to fit since they just rest under the hood).