Cardio, cardio, cardio.
You will be bruised up. I had a coworker pull me aside and ask me if I was lying about what I was doing. He thought I was a victim of domestic violence.
Your shins will be messed up for a long time from making contact with the pads and your sparring partners. I couldn't feel my left thigh for a couple months from eating kicks. Make sure your form is good and that you are countering/absorbing the kicks correctly. Eventually your body will acclimate and it won't hurt as bad.
Also know the difference between extremely sore and injured. I broke a toe, got stabbed with a training knife right below the eye, was kicked in the head, got my neck wrenched, etc and would shake it off, tape it up and keep on but when I snapped my wrist I called it. You will get injured... it's not if, it's when. If you are truely hurt don't let your ego get in the way of saying you need to rest and/or go to the doctor.
Who are you taking Muay Thai from? Are you in the Virginia Beach area? I used to take Jeet Kune Do from Wahsei at Eastern Academy of Martial Arts and then again for a very short time from Eric Haycraft here in Louisville.
I still miss it like crazy but I can't afford the injuries anymore.