See a rheumatologist. I had the same sort of thing. After six months of a fitness program, when by all rights (and according to my recollection of my 20s) my muscles should have started getting in tone and not hurt, I was still aching as if I had just started exercising yesterday.
Finally saw a rheumatologist. I have rheumatoid arthritis. I'm on Celebrex and Methotraxate. It's made a world of difference.
I'm not saying that's your problem, but it's certainly a possibility.
How old are you? I'm 57 (56 when it started).
LRod
Master Woodbutcher and seasoned termite
Shamelessly whoring my website since 1999