Sorry for late reply!
You want to convert Q1 character models to Q3, right? I haven't done that, but I imagine it would take some extra work before exporting to MD3. If I remember correctly Q3 models are separated into several parts to allow them to rotate freely, but the animation is vertex-based like in Q1. So what you'd likely need to do is import a Q1 model into Blender with the MDL import-export script, duplicate it however many parts a Q3 char has, make separate body parts out of those duplicates by deleting unneeded geometry and filling the holes, and then export it with the MD3 exporter found here:
loga_m
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