I had a problem when before installing the VPK I made directory APTR1007/Media with game files and it wasn't booting correctly, I checked the app directory and there was APTR10007 (with 3 zeroes instead of 2) moved my media files from APTR1007 to APTR10007 and it booted. By the way thank you very much for your hardwork.
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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!