do not cut and paste your modified files throw them on all at once and assume its good! :P
I took all my files for my UPgrade theme, threw them in the right folders, applied the update.zip wasnt able to boot. after hours of trouble shooting, the way i got it to work was put the original apk in the right folder, then applied it to make sure it wouldnt break it. Once i knew it was good i had to modifiy the apk while it was still inside the zip...