Well, this isn't the best forum for this (General Discussion would be better since more people will respond to the thread there), but I might as well help as much as I can.
Look up Quark 5. Version 6 apparently has problems converting to Q2, but 5 apparently works well. People have posted tutorials on the net in various places, too.
When my computer inevitably explodes and kills me, my cat inherits everything I own. He may be the only one capable of continuing my work.
Quark 5 converts them just fine, you can simply select 'save as...', select .md2 from the list and you have a fresh .md2 for your modding pleasure.
I couldn't quite get the skin converted to the q2 pallete though, so the colours were a bit messed up.