I was questioned by an ICE agent?

We do not know. You need to hire an Immigration attorney who will contact ICE or DHS and see what they are up to.

US visa

Each country has its own rules. Why were you denied? If the same reason presents a problem for the US (shared information or not) you will likely...

Is there a way to get some kind of assurance from employer and immigration attorney that they will not withdraw earlier I140?

No. However, a new proposed rule, when in effect might help you in case they would want to do something like this.

Is there any travel permit for emergencies for wife of citizen waiting for 485 interview?

You should be able to get an advance parole, but you need to consult with an Immigration lawyer to see if you can travel at all.

Am i still eligible to work in US.

You need to address all questions about your status to the company's lawyer who processed your paperwork.

Just affidavits are usually not enough. Look for other evidence: maybe your friends took pictures of you, maybe you have tickets, envelopes, etc.

Claiming US citizenship, born overseas in US hospital Gorgas, in 1986 by a father from the US army and mother married to him .

First, you need to collect all the available records first. Then, you need to work with an attorney.

How to get a R-1 visa with an OPT status?

The church would have to petition for you and you will need to change our status.

What visa to get for adopted niece?

It would be an Immediate Relative visa, but the problem here is that the International adoption may be completed in different forms with different...

Time in Removal Proceedings and Immigration(or Unlawful Presence) Clock?

If you cannot prevail in your proceedings, you will have a bigger problem then "unlawful presence". Consult with an immigration attorney ASAP.