Permission issues on recovered user data

I got in a A1226 with a failing hard drive. It also has a bad optical drive. The machine would not fully boot. Put it in Target mode with a 2009 A1278 and tried to repair the drive. Disk utilities reports it's unable to repair and to back up the data. I get a new Seagate Momentus XT and hook it up to the A1278 using a universal adapter, format the drive and use SuperDuper to clone the drive. Use another adapter to hook up the bad drive. The user folder is massive with to many corrupt files to use drag and drop or migration asst. So I use a combination of dragging the Desktop file and documents and later Mig. Asst. to get most of the User folder. Put the new drive in the A1226 create a user with the old name. All works well when logged into the migrated user except the things that were drag and drop. Again the Target Mode with the A1278 I'm told I don't have permission to open those using Disk Utilities. I can't run repair permissions because the disk is set to ignore ownerships. Any ideas?