What to do if I am separated, pregnant with another man’s child and want a divorce?

You can put your boyfriend's name on the birth certificate now.

Technically, your husband could challenge this and would win under the California presumed fatherhood statute (Family Code 7611).  There are similar code sections in most states labeled the uniform parentage act. 

The easiest way to get a divorce is called summary dissolution but most couples (including you) don't qualify for summary dissolution.  If you had children during the course of the marriage (even with someone else) you are not eligible for summary dissolution.  You can read more about summary dissolution here: http://www.courts.ca.gov/documents/fl810.pdf.

You need to file a Petition for divorce (FL-100)...remember to request that your name be restored (if that's what you want).  You will also need to file an income and expense declaration (FL-150).

After filing the FL-100, you will serve it on your husband (at the same time send him your FL-150 and a FL-140--yes that's new and you haven't filed it with the court).  If he is agreeable you can serve him using the notice and acknowledgement form (FL-117) instead of using a process server. 

After you served all that on him and receive his acknowledgement, file a FL-141 form with the court, stating that you served the FL-140 on "other": notice and acknowledgement.

He then needs to respond, pay an appearance fee, file his FL-150, Send you an FL-140, then file an FL-141 with the court.

Before getting a final judgment, you should final final declarations of disclosure and send new FL-140's to one another, both filing new FL-141's after. 

Then you and your husband can finalize everything using either a Marital Settlement Agreement or Stipulated Judgment.  Almost every county in CA has specific local rules governing Marital Settlement Agreements and may have specific forms.  Most lawyers prefer a stipulated judgment because it is enforceable when entered into until signed by the judge.  Either way you would submit the FL-180 Judgment form along with either the Marital Settlement Agreement or Stipulated Judgment to the court. 

In part, depending on local rules, you and/or your husband may need to go to a prove-up hearing where the judge will make sure you both want a divorce (and that you are real people that exist).

Oh and along with the FL-180, you would also need to submit an FL-190 for each party.

Is your head spinning yet? 

I think the short of it is:

1) You probably should have done this years ago;

2) It is much easier if you get an attorney;

3) If you are adventurous enough to go out on a limb and represent yourself, there are a lot of books out there and you need to buy one of them because this is rediculously intricate stuff.

Best of luck.