I was in the same situation a while back. My body ached all over like I had the body ache flu. And the morning rise sucked like u said. I feel like that everytime I dont warm up right and blast through my sets. So in my case, I took 4 days off and felt good. I try not to over train and its worked for me. 8 hrs. sleep a night is a MUST! So try to get it. If you know you got the 8 hrs, you feel alot more rested. They say advil hinders gains, but I take 3 pills for aches now and then, and still gaining weight. Could be that Im not taking enough to hinder gains, not sure.
Anyway, thats my experience with aches and pains. Good luck!