None of the method calls show up as huge consumers of time (other than some the SWIG logic).

I'm concerned that if we broke the libraries down any further then we'd just exacerbate our method call overhead issue.

Yes, it is a whale. I believe we have a handle on it, given two large scale profiling runs, I simply don't know how to measure things beyond what the profiler provides. (if that is even our issue to begin with).