it would be nice if PCS gave you some clue as to were those 'too close' polys were, like "one or more polygons with identical centroids located a x,y,z, please do something about it", I have a feeling just jerking a vert 0.01 units in any direction would probly fix the problem more oftine than not. though in PCS2 this problem would have a much more eloquent solution; you could color every polygon that had identical centeroids, you can do this becase PCS2 will load and display models before it compiles them.
PCS also has a problem in that it has a staticly allocated geometry buffer, initaly there seems to be no way to fix this as there is no way to tell when you start the conversion process how big it's going to need to be, but I think you could just fill up the buffer get a new one twice as big copy the old one into the new one get rid of the old one and move on, I doubt this would be too hard for someone who has intimate knowledge of the source, unfortunately not even Kaz has that anymore as he hasn't touched it in like two years.
