I had Eric Gorr bore my 02YZ125 to 134cc and port it. I asked him to give the bike more power everywhere, which he did. It pulls better from lower rpms, offers more over-rev, and is way, way easier to keep on the pipe. His prices are very competitive as well. Eric will work with you on getting you the most effective set-up to meet your needs. I wanted to keep my bike AMA 125 class legal, but having it bored further wouldn't have cost much more. I'm running the stock pipe. I've experimented with the FMF Fatty and Pro Circuit pipes, both of which gave questionable improvements to power before the porting, are significantly less effective after I had it ported. The stock pipe seems to be the way to go on this bike.
Before the porting I switched to the European spec needle; really cleaned up the jetting. A friend installed V-Force reeds ion his 02YZ125, which helped his bike a little, but nothing like the porting/bore.