How can I get permission to access my own files?

I recently got a new Mac Pro, and I used a Time Machine backup to migrate my data. Then I discovered that Time Machine doesn't actually back up everything; it leaves out all the "Build" folders in all of my Xcode projects for some reason. I transferred all those folders manually, but I couldn't help but wonder what else Time Machine was omitting. So I decided that before I permanently retire my old computer (a seven year old iMac), I'd make a full backup of all its data onto BD-Roms. This it turning out to be quite difficult.
First I tried using Target Disk Mode and running Disk Utility on a second computer to create a disk image. But after about 15 hours, it wasn't even a third of the way done, so I cancelled that. Then I tried connecting an external drive to my old computer and just dragging all the files onto it, which seemed to be working at first, but then after a couple hours, it said something like, "You don't have permission to access the Keychain App," and it stopped transferring. So I tried again, but I omitted the Applications folder, since that's where the Keychain app is. Then, after a couple more hours, it said something like, "You don't have permission to access some other file."
Is there any way I can disable this permissions business? I tried going to "get info" and giving everyone read and write privileges, but it didn't make any difference. I wouldn't even mind just skipping the files with permission issues, but the problem is that whenever it gets to an "unpermitted" file, it just completely bails out of the whole transfer and then I have to start all over again. Is there at least a way to make it just skip those files and go on with the transfer?

Not in your case. System-level folders cannot be backed up by drag-copying; just drag your home folder to the external drive.
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Thanks for your replies ckuan
I agree with Tgod that your first solution does not work. It appears unpredictable whether the old or new file names are listed when you drag the folders into iTunes from Windows Explorer. The folder structure is completely missing. I reckon if you have to muck around spending days/weeks/months finding out how to fix links to a secret meta-file (obviously designed by some deep-cover microsoft worm working in the Apple!), then it's pretty obvious that almost any alternate way of doing this would be better. Bye bye iTunes!!
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How can I get permission to access my own files?

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