I cannot help you directly, but at least I can tell you this: Several years ago we replaced some matlab functions (from the optimization toolbox) with self-written C+ function and called these instead of the matlab functions. We experienced a speed-up of 20-100 times faster calculation. Which, in our case, meant hours instead of days of calculation time.
I don't know if this experience is still valid with the recent Matlab versions, or if that applied to the optimization toolbox only. But since, as far as I understand, Matlab is a script based program, it is not the fastest possible way to do calculations. I would guess that your problem could be faster calculated but you would have to do it on your own if you do not find any C code. And, because Mathworks tries to improve the calculation efficiency all the time, the advantage might decrease with every version. So you will know how much time you can save only by trying for yourself (and also it depends on your specific problem, of course).