You need to consult in person with an employment attorney. Your questions are too complex for this simple Q&A forum and more details are needed to provide guidance. Go see one or more lawyers. Bring any paperwork you might have.
"Whistle-blowing" is a far narrower and more limited legal protection than most non-attorneys understand, and it is often determined only after-the-fact to be inapplicable to a specific employment circumstance. No one should act in any manner that risks their employment in reliance on the expectation that they are protected as a whistleblower without first obtaining skilled and experienced legal advice, just as Ms. Goldstein has cautioned.
My responses to questions on Avvo are never intended as legal advice and must not be relied upon as legal advice. I give legal advice only in the course of an attorney-client relationship. Exchange of information through Avvo's Questions forum does not establish an attorney-client relationship with me. That relationship is established only by individual consultation and execution of a written agreement for legal services.