I intend to create a Epub3 rendering engine from scratch(preferably in C++) but am clueless about where to start.Is there a good starting point for such a project or resources that would help me get started. I have some prior experience with such engines(for Epub2 and PDF) but not in depth knowledge.
Sounds like a big project, but if you have experience writing engines for ePub2 and PDF might be manageable...
The best place to start would be the Readium SDK (http://readium.org/projects/readium-sdk). Then you could just work through the spec (http://www.idpf.org/epub/30/spec/epub30-overview.html) piece by piece. I would highly recommend building in WebKit because most of the functionality you need is packaged in there...
The spec itself is basically just a browser, so another good place to start might be with some browser research (Mozilla etc) and check out some SDKs on that front.
Best of luck!