Flowers come from a sheath at the top of the cane between the leaves. Usually root growth starts when the new growth is very small ( for me anyways ). I'd wait until you start to see the root nubs coming out of the rhizome and repot then, but it sounds like you are very close.
Do not be in a hurry to repot it until the new growth is fairly tall. As Stephen pointed out, this species does not initiate new roots until the newest growth is nearing its completion. If you repot C. amethystoglossa when you see the new lead break from the base of last season's growth, you stand an excellent chance of killing the plant, or setting it back severely if it survives being repotted at the wrong time.