Being sore at the sight of the injection is common and with her being so tiny, that could be why she seems sore all over. I'd say give your vet a call and let them know and ask for their recommendation.
I agree with others to space the vaccinations out 3 to 4 weeks. I took Riley in on a Saturday morning for a set vaccinations. It was only one shot but it was one of the combo vaccines. He didn't start having a reaction until about 9 - 10 hours later... broke out into big red hives and was all swollen... so we ended up in the emergency vet that night. I called his regular vet when they opened that Monday to let them know and his Vet Recommended to make an appointment for vaccinations at the beginning of the week first thing in the morning. That way if he has a reaction I can take them back into their office. He also said his next visit we will just do "Titers" which are tests that can tell you whether or not your pup needs the booster.
TITER TEST
After Riley's reaction as far as I am concerned he will get his Rabies and that is it. It was very scarey and I Hated seeing him so uncomfortable.
