well,what kind of warm-ups you do before you start freestyle? do you do any moves before freestyle which opens hangs in your legs?
try this when you start freestyle after a bit pause: do a warmup (can be 10min) which includes running,some moves and short stretching.
your legs will be more ready for freestyle=)
also,when you train a lot some day,do some schretching in evening (long moves) next day your legs doesnt hurt so much=)
if you want increase stamina,do 30-60min long run with speed you are able to speak normally (not too fast and not too slow)
hope this helps and ask iy you didnt understand something=)