Filed in South Dakota, but primary business is in California
Typically speaking, a company must be registered in the state(s) where the business is being conducted. In this case, being the business is going to be conducted in California, it seems like you would need to be registered there. You can file your South Dakota business as a foreign entity in California, which will effectively have your business registered in both states.
The federal tax id is obtained through the IRS, so that wouldn't have an effect on the state of registration. A sales/use tax would have to be obtained in the state where the business is conducted (if one is needed).
It would definitely be a wise suggestion to discuss your business plan with a licensed accountant.