Can't get mac back to how it was following manual restore from Time Machine

My MBP, 13-inch, early 2011 10.8.4 has an SSD to boot from in HD bay and a HD in the optical bay where I have my user folder. I dropped the mac when it was switched on and the HD got screwed up and I consequently had to initialise it. The drive is fine now and I had a Time Machine backup form an hour previous so thought I was OK. However, it seems I've been using Time Machine wrong and I couldn't restore things from my USB - I had to go to the latest backup manually in TM and bring the info back.
OK, so everything is back on the drive BUT, I can't get my Mac back to where it was before the drop - It's pointing to the User folder as before but the Mac looks like it's fresh out of the box. Any idea how I can get back?
This is most frustrating and I would genuinely appreciate any help.
Many thanks, Craig

The first thing you need to do is have it tested for a hardware fault.

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