What would be best case in this scenario and what needs to be suggested to the company to do and go for.

You raise too many questions for this site. You should consult with an experienced business immigration attorney.

How can I ensure that I will be able to return to the US, despite my lengthy stay/s on ESTA?

At some point the CBP officer at the airport may give you problems getting back into the USA. Do you tell them that you are visiting on business...

Can my husband adopt my daughter so that she becomes an American citizen or do I have to file for her citizenship on my own?

As a stepfather, your husband can file immediately for your daughter.

Could we be called for an interview due to short nature of marriage? 485 is under EB2 category using CC.

This should not be an issue but you never know if there is an interview if this subject will be raised.

My US citizen biological mom petitioned for me. Can I petition for my step mom? My step-mom & dad were married before I was 18.

Yes - as long as you can document all that you say.

I do not believe that Medicaid benefits will be an issue.

Birth certificate issues for green card application

You will require your birth certificate as well as documentary evidence regarding the other name you use.

Can my wife on F-2 visa earn royalties on a book she wrote?

Your wide directly cannot receive the royalties but there may be other ways to do this.

Is is normal to interview employment based applications like marriage based?

Since this is not typical, you should definitely have counsel present at the interview.

I about to apply for citizenship, my wife overstayed her B1/B2 visa. What should I put on the form for her status?

You can out down "B1/B2 OOS". There should be no issue with that.