Help! I've screwed up my W7 bootup!

I recently had bootup problems and followed the guidance from Imran m in this thread:
Windows 7 stuck at loading screen - Microsoft Community

However, I followed all the steps except I forgot to delete the pending.xml and reboot.xml files. So now my laptop boots but after the W7 logo I get a black screen with a cursor. If I bootup in Safemode it boots but I get just the words safe mode in each corner of the screen. I then tried to boot to safe mode with Command prompt and managed to delete reboot.xml, it couldn't find pending.xml, but still can't get anything except as I've described.

Is there anything I can do to get the system back?
Is there anyway of reinstalling the Windows system files without erase my documents
I have a Recovery disc but if I use that It will erase my documents won't it?
I can boot to command prompt in safe mode and can navigate to my documents folder and see them but I have no way of copying them or is there?

Can anyone help?
Thanks
Tony

Troubleshooting Windows 7 Failure to Boot
Work through that.

If it doesn't work, try this to rescue your documents.

1)Insert USB Flash Drive into your PC.
2)Boot to command prompt and type "notepad" without the quotes.
3)Press File-Save and locate your documents. Expand the Computer subcategory on the left pane of Windows explorer, and drag on drop the files from your PC to the Flash Drive.

After you have recovered your files, I recommend doing a clean install of Windows 7.
Clean Reinstall - Factory OEM Windows 7

Step 10 in the above tutorial Troubleshooting Windows 7 Failure to Start shows how to rescue your files via various means. They are never lost unless the HD fails completely.

I downloaded Paragon and burnt it to a DVD and was able to copy my files (great little piece of software, a godsend!)

I tried a System Restore again and got it back but the boot up was intermittent, sometime booted up on switch on but then next time just got cursor. I ran CCleaner on the registry and noticed that one of the errors was Missing Startup Software %windir%\system32\conime.exe. Could this be the problem?

Run a few Startup Repairs to see if it finds anything to repair.

Thanks I tried that and it didn't find anything :-(
Tony