It doesn't sound like typical pregnancy symptoms. Maybe you have a bug. Pregnant women are more suseptible to tummy upsets. That's why food should be reheated to piping hot or made fresh. It's a pain.
I did not have chills (was always hot as hell though, sweating, etc) but I DID and do still have the runs. The runs got a little better after starting to take Prenatal Vits though.
Call the DR.
I had the chills, especially at night. All of a sudden I'd wake up, teeth chattering -- in July -- and had to use a wool blanket to get through the night. I had it with my previous pregnancy too, very early on. I don't think I was running a fever, but if you are, you should call your doctor ASAP. I also had soft stools, but not the runs. I've read that chills are not completely uncommon in pregnancy. If you have muscle aches & pains, you really need to call your doctor (ie, as in the flu). Otherwise, it might just be pg symptoms.