Tom - it IS a freeware programme, so may not do everything you need, but I daresay a lot of expensive ones wouldn't either.

MuseScore WILL load MIDI files and convert them to notation. I just tried with an early music file from the web. It loaded as three part staff. Don't know how accurate the transcription is. It also will save dots as a MIDI.

It seems to have some form of note entry via midi keyboard http://musescore.org/en/handbook/note-entry but I do not use a midi keyboard, so have no idea how effective it is.

What MuseScore does do is read and write MusicXML which allows you to work with other programmes that also use MusicXML.

As I say, it might not be what you need, but it is worth checking out if it might do enough to be of use.

Quack!
Geoff.