My engine doesn't move that much now with new mounts, but it does move at least an inch.
If you replace all your mounts, flex will be reduced. Until then, plan for some flex. You don't want your box or pipe tearing loose, and you don't want force applied to the throttle body. If you want to attach the box, don't use a rigid pipe. Use INTENSE-style tubing instead.
If I ever do a CAI on the SLE, it'll be INTENSE-style tubing feeding a CAI. Too messy in the winter around here to run a FWI, and the 92-99 doesn't have the 'under skirting' in the fender area to keep a FWI clean like the 2k+ do.