Has anyone tried Gibson Assembly Optimizations? Has anyone tried the chew back-anneal in vitro DNA assembly method (known as Gibson Assembly) for difficult sequences, like GC-rich sequences? How big constructs could you efficiently assemble? Did you use the original protocol or some optimizations?

I haven't tried Gibson Assembly myself, but I do know the Cambridge iGEM Team in 2010 and 2011 developed a web-based tool - Gibthon \- for automatically generating primers for Gibson Assembly.

You could try running your difficult sequences through their tool to see what it suggests for primers. It apparently gives you a "value for the Gibbs free energy of the worst case secondary structure of the primer."