I decided to indulge in my new favorite vice : before getting down and dirty with C, write a high level Perl prototype to spot the potential bugs and hurdles and make the C code writing easier.

That's an excellent strategy (hardly a "vice" but I think you knew that :-) and one which would serve anybody well. It might be interesting for you to benchmark both solutions to each problem you tackle in this way as that will give you a feel for what level of performance boost you could get with C compared with the extra development effort - a useful experience to acquire.