Speak to an employment attorney.
I am not a lawyer, but you have clearly been discriminated against for your pregnancy. If your pay was lowered, you also have demonstrable damages. Based on what you've said in your post, a lawyer can probably point out a whole lot more labor law violations too.
Do not speak to HR. If you intend to sue your company (you probably should, but again a lawyer can advise you better), their job is to protect the company from you. Even if you don't plan to sue your company, HR will be hesitant to take action against the owner of the company when they know there's a high chance they'll face retaliation, legal or not.
You may be afraid you're burning bridges. You're not; your manager cannot be relied upon to give you a good recomendation anyway (unless a court forces him to), and since you're competent, you can find a job with much better working conditions.
