I daily take vitamin supplements because I have a very low metabolism and am prone to fatigue. I know I mustn’t take pills on Shabbat but I then feel very weak and am unable to complete prayers with 100% energy and Kavanah. Can I take the supplements or is it better I struggle throughout the day and not take them?

Generally, healthy people should not take vitamin pills on Shabbat. From the description of symptoms you list you are a "Cholah" and may take the pills on Shabbat. If you can consult with your local Rabbi about any limitations of taking pills, please do so.