The .46 will also require you to use .018 lines. If the plane finished out anywhere under 50 ounces, I would go with the .40. I have flown a Super Chipmunk quite a bit with .40's and .46's, and i like the smaller lines better. If I felt I had to have a .46 in it, it would be a classic ST .46. Properly trimmed, that combo can handle the extra drag of the .018 lines, I think.
What kind of kit is it?
Good luck and have fun,
Dan McEntee