This is actually not so uncommon. You have to be forgiving on yourself. You said yourself you haven't done much exercise. What you are experiencing is Delayed Muscle Soreness. Fancy name for exactly what is implies. You worked muscles that you haven't directly worked in a long time, of course they will be sore. This is a good sign too, when they are sore. That means you worked them hard enough!! You need to give your muscles time to rebuild themselves. All beginner and experiences people who workout need this. Its just science. When we work out we are actually tearing the small muscle fibers. With proper nutrution and just a day of rest what those fibers are doing are repairing themsleves....bigger and stronger. Its like shaving your legs. The every time you shave the hair grows back darker, but it takes some time till they Do grow back and you have to shave again. You see?
You should probably do your strength exercises every other day. You'll see better improvement. Plus you'll be more motivated to go at it again when you're not still tired from yesterday. And if you're doing cardio, you could alternate the intensity to give your joints a break too. Like jog one day, walk the next.
Also think about building up to that intensity level. There are plenty of ways to modify sit ups or any other exercise untill you are strong enough to do the regualr way. Don't ever feel bad about modifying an exercise either. You're actually helping yourself. If you've never run before how do you expect to run a marathon? By working up to that piont!
good luck!!!!!