Cadence and saddle height spring to mind.
Are you a masher, pedal In a high gear or a spinner, with a faster cadence. I think 90 rpm is a good cadence and it might seem counter intuitive at first but it can make a big difference, much easier on the legs.
Saddle height, too low and it hurts the thighs like hell, been there done that. You feel like your thighs are going to catch fire.
It also sounds like you're doing a lot in your first month although the intensity you're doing it makes a big difference too.
25 miles every other day, plus weight training, plus walking a lot at work, youre asking a lot of yourself. I'd do the 25 miles at a steady pace, let your muscles build slowly.