You've taken too many details out of context so that it is hard to ascertain what is right and what is wrong. I just to want to point out several things:
1. Judges have absolute immunity against civil liabilities. This is essentially a heritage from common law but it is important for the check and balance system of this country. Immunity does not mean the judge can do anything he wants. He must obey certain legal doctrines such as stare decisis. He must not act impropriely. He must comply with Code of Judicial Conduct or he can be disciplined. It is hard to tell if the judge acted improperly without knowing all the details. However, when you learned he has connection with the other company did you move to disqualify him? If there is damage, did you try to get a jury trial?
2. There are so many equivocal information in your text which makes it really hard to tell the right from wrong. For example, you said when the S Company filed summary judgment there were disputed matters. A summary judgment is granted when there is no genuine issue of material fact and the moving party is entitled to a judgmen of law. FRCP 56(c). It does not mean summary judgment cannot be granted if there is any dispute. The dispute must be to a material matter in the case. A judge has lots of discretion when granting or denying a summary judgment and if he thinks there is no dispute on a material fact then it should be granted.
3. When you wrote you showed the $600/hr IP lawyer the brief opposing the summary judgment, he totally agreed. This is very confusing. The lawyer represented you in court and it is his job to write the brief. Why did he do that?
4. FRCP 24 permits intervention as of right and permissive intervention. You said previously the fight is between two companies so that the judge can be under his discretion to treat your motion as permissive intervention. Again, it is permissive by the court and he can deny it if he sees it.
5. There is no such thing as FRCP 54-6, unles you cited something else. You have the first appeal as of right and you give up. Attorney cost is also a discretion by the court and there is no such thing that you have to prepay the other party's attorney cost in order to appeal.
6. You said to rule in favor of the other party the judge had to reverse laws. This is confusing. What laws? Federal statutes? Case precedents? If it is a statute, a judge cannot rule against it unless on its constitutionality. If it is case precedent, is it on point and binding? If it is not on point, it is not binding even if it is from the same jurisdiction. If it is binding, a district judge cannot overrule it, per stare decisis.