Let's see now....
Stock is 17/45
With the wheel swap, you need 17/41 to stay 'stock'.
You're proposing a 17/39.
My opinion is, if you put the 17/39 combo on the stock wheel, you're going 6 teeth less, which is a pretty big jump. IMHO, you're going to be slipping the clutch a lot to get going, and you'll just be running around in 4th, say, rather than 5th all the time.
The 17/39 combo on the wheel swap will be much less severe, dropping only 2 teeth from 'stock'. Much more livable.
My two cents.
Good luck with it, whatever you do.
Kirk