Well lets see, I am currently looking to do the same kind of thing and this is how I look at it...

1) www.visiv.co.uk -> Get the 30 Day trial - or real version if you want to spend money -> This will scan the music in, and save as MIDI.

2) www.anvilstudio.com/upgraden.htm -> Free unless you want extra features (like printing) -> Use this to transpose the score.

3) www.notation.com/MidiNotatePlayer.htm -> get the free (indefinite) version -> use this to print unless you paid for Anvil Studios...