@prchakal I feel your pain.
It took me about 2 hours to get my previous Box2d project to link with the latest cocos2d 3.0. Here is what I had to do, not sure if it is correct yet but at least it is linking, I have some other problem in running the game:
For Visual Studio 2012:
Right click on libChipmunk and remove if it from the project exists.
In Project properties change the CC_ENABLE_CHIPMUNK_INTEGRATION=1 and replace it with CC_ENABLE_BOX2D_INTEGRATION=1
Add the cocos2d\external\Box2D\proj.win32\Box2D.vcxproj to your project.
Right click on the solution and under Common Properties click on Project Dependencies.
Right click on game project and under Common Properties click on Framework and References
In References should be libAudio, libcocos2d
Click Add New Reference and select libBox2D
Do not define CC_USE_PHYSICS , all this code depends on chipmunk (you might be able to leave the libchipmunk in the project and skip this part)
I used the cocos2d\tools\project-creator\create_project.py to generate my project. Loaded up the \Game\proj.win32\Game.sln and after making the changes above was able to get my Box2d game compiled and linked with 3.0 (using the latest from github).
It took a little longer than usual since I haven't used VS2012 much, still stuck on VS2008 at work.