You've got your directories crossed there! The Media.zip needs to be uncompressed and installed into "ux0:app/APTR1007/Media" and it's "portal_pak_dir.vpk" that needs to be copied to "ux0:data/AptrRecon".
Do checkout the video from The TRON if you have trouble with this as it goes into the install process in detail, and please tell me if you manage to get it going!