Vijay,
You are proabably best off starting with the OOB WM 6.2 and then selectively bringing in your changes from WM 5.3. This is especially true if you are using Windows clients as the Windows screens have been updated to be more like the tablet screens.
Another big change is that the Java has been updated to use JCo 3 now so there are a number of changes related to that as well that will make starting with WM 6.2 the right choice.
--Bill