Hi Caroline,
I had a similar experience with my twins. I got the bill from their 2 month shots, and it was $1,000.00. We learned our insurance through my husband's employer does not cover vaccinations at all.
Our solution was to go to the county we live in (kendall) and we were able to get the shots both our babies needed for $120.00 total for both babies for their 4 month shots. We also went back there for their 6 month shots. It is $20.00 a shot and we just had to sign a form that we are under insured because our insurance does not cover shots.
We were grateful this service is offered through the county and I understand most counties have programs like this. You may want to check into that. Good luck with the insurance, I am not sure I can offer any good advice there.