I think the most important thing is actually to make sure you don’t get too tired. If I exercise too strenuously, I find that my Candida symptoms get worse. I try to exercise to a point where I can stop and still feel refreshed. If you are exhausted then you’ve done too much.
As for the time of day, I don’t think it really matters. Just don’t fight your body clock. So don’t get up too early or stay up too late to exercise.