Thanks everyone for your help.
I discussed it with my ABAP consultants and here is what they said :
1) 1) Should take SE16 dump project object wise, e.g. one dump for Project Definitions, one for WBS Elements and so on from 4.6C system
2) 2) Create an Excel template for each one of this
3) 3) Use BAPIs for each object and write custom program as per the new requirement
4) 4)Execute it using LSMW in Development with some test projects
5) 5)More projects in QA
6) 6)Finally upload it in Production system
7)
They have never used a third party tool like Winshuttle for this so, not sure how helpful it could be.
Have not decided on the planned cost upload as yet, this was just for the project structures.
Any comments/corrections are welcome.
Thanks.