Yes, in the first four weeks I felt as though I'd been dragged through a hedge backwards, repeatedly.
Muscle aches can be caused by not enough salt because IP food isn't loaded with sodium the way regular pre-packaged food is you may be suffering from low sodium. Try a half tsp of salt on the back of your hand and lick it. Remember to keep a glass of water handy as the salt taken neat may make you gag a little.
(one of the times you wish the tequila was IP compliant, right?)
Try some gentle stretches after being active, and a soak in a hot bath before bed to relax all your muscles.
It will get better.