Is there any best practice? Or perhaps how should you do it. To keep the original key or not, while playing a solo piece.

I have several pieces by Bach which I would like to perform and possibly also record. If I do record two versions and the one in one octave lower sound better my feeling is that I should keep this. Since it sounds better, right?
My instrument, the clarinet was not invented until around 1750.

If I would play "bach chromatic fantasy" for keyboard am I free to 

1. Change key to another key, better suited for my instrument.
2. Change octave (if I would perform on a "bass clarinet" this would obviously be an octave down). But in that case, can I keep this octave as long as my instrument can handle it. Lets say Bach wrote a piece for flute. But then the upper notes are hard to play. Can I change the octave.

I realize that changing octave and key is going to make an unprofessional impression, perhaps. But then again should I go with conventions - even if it sounds worse - I think not. I am leaning towards keeping the original key but one octave lower. But then again. If only a fifth (or a third) would perhaps be the best of all. But Then I perhaps have passed the line conventions puts on me.

A practical example. I am a trained clarinetist and a trained flute player.

3. Let's say I play Bach's solo flute sonata. If I chose the octave one octave down, I can play all notes except one, the very bottom note. I really have to practice very hard to make it sound good in the original octave. - How much "artistic freedom" - do I have?