Is it normal to feel run down and fatigued after having a high junk food (simple carb) diet then switching to a low carb healthy one? If yes, how long?

Healthy living. No. Actually. Are you eating enough total calories? Getting a majority of your calories from proteins? Checked your thyroid and vitamin d levels?
Yes. Your body is used to the extra calories and will take a few days to a few weeks to adjust.