Emplyr changed pay in 2013 frm biweekly to 2X monthly & withheld 2 weeks of pay, payable when employee leaves. Was this legal?

One problem you're going to have is that this was three (or so) years ago and, as such, the SoL on complaining about it may have run.

Do I have a case; how do I begin to file an EEOC case against my employer (mediation requirement first)?

It does sound like you a cognizable ADA claim. You should consult with an attorney prior to filing your charge and, that is especially true if you...

Assuming you can physically perform the job, I suppose you could do this. Obviously, the other way of proceeding is to file a charge with the EEOC...

Is there any legal action i can take against an employer who consistently bounces paychecks?

There are a number of illegal practices going on here. You should consult with an experienced wage and hour attorney.

Can an employer legally take my vacation and insurance pay from my check AFTER payroll was already done?

From what you have said, I don't see any problem with it.

Can this be considered a form of discrimination? Do I have any recourse against this federal agency?

I think you would need to know why, specifically, they have denied you these opportunities. If it is for a reason prohibited by the civil rights...

Is the owner required to take out taxes because she never has and does not intend too?

In addition to the tax issue, I really wonder whether you have an overtime lawsuit that you could bring.

This certainly sounds like a potential violation of the pregnancy discrimination laws. Your should seek out counsel.

Do I have any rights? Is my employer allow to give me the option to take a pay cut or get ? I'm the only one that got a pay cut.

It really depends on a lot of facts not discussed in your post. You need to consult with an experienced attorney in order to get a good answer to...

Can I do that without getting into trouble?

You really need an attorney to walk you through the issues and your options. There are a variety of possible, and potentially lucrative, legal...