Looks like you're in luck. I originally had this song transcribed for alto sax, but by just transposing it to concert pitch and putting all the notes an octave higher, I've made it possible for flutes to play it too (I think).
https://drive.google.com/file/d/0B0uVTddyzs4saW42UmFOdm5ZcGc/edit?usp=sharing
I don't know a whole lot about flutes, so please let me know if you see any problems in the sheet music.
Glad you liked it! I wrote it especially for the upcoming 20th Pokémon anniversary, which I hope I complete and submit around then.
As for the software, I use Finale 2012 (http://www.finalemusic.com).