A repair should do the job, but keep in mind if this is temporary then the repair option is a good one, whereas if you plan to stay on the box for a long period, best thing to do is a clean setup.
I was able to complete the job. Not with the repair option at first instance (which goes into DOS prompt). I got stuck up here, trying for all the options for a long long time. But continue with the setup, and when the system identifies that there is already existing windows installed, it prompts for option to repair the same. Say Yes, and the rest is happy going. Though it deletes and then adds lots of system files, the existing files and applications are intact...100% as was working in the previous system. I am very happy to find every thing intact, as i have lot of applications, for which i do not have the setup files to reinstall. So i was ready to take trouble in finding an option to move the same HDD as it is. It was worth spending the time in finding a solution and not giving up! (or rather wasting time as some people say)