Go consult with an employment attorney. There are ways that you need to proceed if you are going to whistle blow in order to protect yourself under the law.
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You situation is likely a bit too complicated to address here. I too recommend that you speak with counsel. There are certain anti-retaliation rights available to you, but you want to make sure you are giving proper notice of the issues so that if you are retaliated against there is a good record of your behavior leading up to it.