SECRETARY OF STATE
The Secretary of State local office is located at 1500 11th Street Sacramento, California 95814, Phone (916) 653-6814, or you can find more information at www.sos.ca.gov,
Once you have your nonprofit corporation number, you may register locally in San Francisco with the Tax Collector's Office for a BUSINESS REGISTRATION CERTIFICATE
To apply for Business Registration Exemption to avoid paying payroll taxes and registration fees,
apply for a Declaration of Exemption from Business Registration Certificate to let San Francisco Tax and Treasurer's office know that you are a nonprofit. Section 2 in this linked form allows you check off "nonprofit"
See this link for more details and reference to code for this nonprofit exemption,
FEDERAL EMPLOYER IDENTIFICATION NUMBER (FEIN)
As for the Employer ID Number, this is a federal requirement, and you can obtain a FEIN from the Internal Revenue Service. Fill out an SS4 form and call the IRS office in Fresno to process by phone or you can file on-line. The local IRS office can also provide you the withholding and payroll tax forms for reporting the income of your business.
When you inquire about the EIN forms, please let the IRS staff know that you are a nonprofit and wish to obtain 501(c)(3) tax exemption status. The IRS will tell you about Form 1023 which is the multi-page form you will need to file. Within three to six months of submitting your paperwork, you ordinarily will receive a letter, granting tax-exempt status to your organization.
Publication "Tax Exempt Status for your Organization": http://www.irs.gov/pub/irs-pdf/p557.pdf
Internal Revenue Service - Fresno (For FEIN) 800-829-4933
Internal Revenue Service - San Francisco (for other IRS info) 800-829-1040
450 Golden Gate Avenue, 1st Floor
San Francisco, CA 94102
Lastly, here is a free webinar to help you form your nonprofit. The tutorial describes 12 tasks you will need to accomplish as part of the process of establishing a nonprofit organization including obtaining a Employer Identification Number and filing for tax exempt status (501(c)3). http://foundationcenter.org/getstarted/tutorials/establish/index.html
The Foundation Center is a great resource for nonprofit formation and grantseeking. www.foundationcenter.org
This is their local office
312 Sutter Street, Suite 606
San Francisco, CA 94108-4314
FUNDING YOUR NONPROFIT
The following lenders provide loans for nonprofit organizations:
Northern California Community Loan
SF Finance Fund
Traditional lending institutions, such as larger banks, also lend to nonprofits.
Small Business Assistance Center, City Hall, Room 110, 1 Dr. Carlton B. Goodlett Place, San Francisco, CA 94102
Phone: 415-554-6134 Office Hours: M-F, 8 AM - 5 PM