Can enterococcus faecalis infection in the prostate cause you to feel tired, achy, and muscle pains, etc?

Possible, unlikely. A minority of prostatitis is caused by bacteria, but E. fecalis is one that can do it. Acute bacterial prostatitis is very painful, often with high fever. Chronic prostatiis causes discomfort in the prostate area, but usually no systemic symptoms. Your symptoms seem to fall between these extremes. My guess is they are unrelated to your prostate, unless due to anxiety about it. Discuss w/ your doc.