[femngi]

You should read http://www.scipy.org/PerformancePython if you haven't already seen it since it deals with the performance of nested loops. The only issue I guess would be portability, for example to PyPy.

[odiroot]

I totally missed this guide. I'd definitely use Cython to optimize this.

Previously I used Cython to wrap original C++ code and it performed really well but I got numerical differences in result.

[fijal]

This does not cover PyPy and under PyPy behavior of those methods will be Very different.