marcus is cetainly right with the general rules, but there are quite a few guys on here with feedback on your bike
what sort of port job are you thinking about rider? check out this thread for more info. dont forget the v-force also, from all the info i have seen, it is one of the best mods for the yz250 (i have one sat on my bench ready for installation)
http://dirtrider.net/forums3/showthread.php?threadid=60221
i run the SST/shorty, i never had the stock to compare, but lots of people like the SST for the YZ. its supposed to bee a bit topendy, but it seems to compliment a eric gorr low to middle powerband very well. i have ridden a couple of stocker since and the differnece in power is quite significant.
but i certainly feel its worth going for the porting and v-force before shelling out on a pipe.