From a legal standpoint what can we do?

If she is being sexually harassed there may be a potential lawsuit. Contact an employment and/or civil attorney.

It really depends if the holes are creating a threat to the children or not. You should consult a family law attorney.

Is there a statute of limitations or a time frame that they have to complete an investigation? What rights do I have?

You should consult a family law attorney.

Do I have grounds for a suit?

I believe you already asked this question, again, you may have a suit. Consult with a civil attorney.

What should I do about it, if anything?

If there is any evidence that they are specifically firing you because you are pregnant you could have a suit. Contact a civil attorney.

Is it legal for the owner of a restaurant to demand a percentage of tips from its employees, of which he's personally receiving?

The practice that you are describing is not legal and you should consult an attorney regarding it.

Is it illegal to alter evidence presented at trial and if so what is the penalty?

The Judge weighs and considers the credibility of evidence, so if you each submitted emails and you made it clear with the original that your...

Will someone help me defend my rights and prove that I am being discriminated against because of my medical situation?

As the previous attorneys wrote, you have no case here as private companies can create their own drug policies for new hires and current employees.

Should i leave the country immediately ? If i book my flight back to my home country, will I be asked questions while leaving ?

Consult an immigration attorney, you have not provided enough facts here to provide an answer.

My question is the status of his release without predudice, how many years later can they come and try to try him for that crime

The statute of limitations is seven years.