How do I migrate from one user to another to resolve sleep/permissions issues?

My MacBook Pro's been having several issues, mainly with waking from sleep. I've tried Repairing Permissions, Repair Disk, running tools like OnyX and Drive Genius, but they can't find any issues. I checked the Console log, and there was some sort of denial from displaying the login window after I woke up from sleep.
Initially I thought this had to do with some of my peripherals being plugged in when I already had the lid closed; the Mac would wake up, not realize the lid was closed, and never go back to sleep. Nothing--keyboard or trackpad touches--would wake the machine up. I'd have to hard reset by holding the Power button on.
I had an Apple Genius suggest that I create a new user and test it out with the (same) default sleep settings as the buggy user account. It wakes up from sleep lightning fast, and has thus far never had any issues.
I'm leaning toward sticking with this new user and migrating over my things bit by bit, to try and avoid potential permissions issues. But since I don't know where the source of this sleep problem lies, how should I go about it?
I've read through Pondini's Transfer Guide here http://pondini.org/OSX/Transfer.html, but I'm just wondering where people would start, knowing that the machine has had permissions issues with some files. (The permissions issues, btw, I believe were caused by a mangled Time Machine restore. I replaced my internal HD with another one, but the Time Machine/Migration Assistant restore wasn't complete. I did it a second time from within the user account that got created, then tried to delete the malformed one and rename the complete one, but that's when the issues started.)

I wasn't intending to move the entire home folder, rather, moving things like what's inside my Documents folder in chunks.
From what I read, tracking down the origin of sleep/wake problems on a computer is notoriously hard, especially if Disk Utility and similar tools don't give any clues during Repair Disk or Repair Permissions. Creating the new user seemed to help, but I don't know why that alone would "fix" anything, so I haven't moved any files as of yet nor done anything with the new user account.
Trying to move the things from my Library folder to my desktop also seems a bit risky; it's hidden in Lion and Mountain Lion because a lot of system files are there, right? Wouldn't moving them cause problems, not just help me find what file/folder (if any) could be the culprit?

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