The Serial class uses a buffer implemented in software that has a size of 64 bytes. You can study Robin's Serial Input Basics - updated to get some ideas how to work around that problem.
But seeing that you seem to have solved the issue, it will be a bit like putting the horse behind the cart 
But it ill be a useful read anyway.
It might help other people that encounter the same problem if you post the working code. It might also be useful to get some feedback if needed.