In the preview of Amazing Spider-Man #5 it states that it was a swapping of minds that Doc Ock performed not brain waves being rewritten in the introduction page...and Slott himself wrote that.
Go to the Amazing Spider-Man #5 preview thread and check it out for yourself.
If you continue to not accept what I've been saying after the writer pretty much confirms it without directly saying that Peter's mind has been cloned even though it has then I don't know what else to say.
Peter clearly died in Doc Ock's body.
If he was successful in uploading his actual mind into his body (as you believe Slott to have stated) then how could he interact with Doc Ock afterwards?
Peter's mind would no longer be in Doc Ock's body to do such a thing had he actually succeeded in uploading his actual mind back into his body. The result of that fail makes Ghost Peter to be the cloned mind of Peter...it's as simple as that.
In order for me to admit that I'm wrong you have to answer the above question in bold print in a manner that makes sense. If you can't then logically you have to accept what I've been stating to be true.