I did my final year project for my degree on physical modeling before this summer. I chose the guitar, specifically electric, and I built my final synth in PureData. Is this what you mean? I can upload my final annotated patch if you want?
I read Julius smith's entire thing on his site, and it took a while to work out how to implement it in pd, especially with delay lines. Built one in Matlab first, then did it in pd because I hate programming in text like with C++. Built a delay with feedback, bit-crusher, analogue/digital overdrive and distortion, as well as ring mod and amplifier feedback loop. I ran out of time, so I didn't get to do pickup design-specific modeling, or sympathetic resonance. I did manage to get different types of excitation (pick or finger etc.)
I've got a pdf of my dissertation hanging around somewhere as well, puts all the physics stuff into laymen/musician's terms
anyway, let me know if this is what you're on about