My fear is something very unexpected happens and I will make the wrong decision to remedy it, crushing ROI or the integrity of the unit/home.

The standard contracts provide guidance and remedies for EMD disputes through arbitration.

I purchased a home out of foreclosure where the prior tenants had used the home to grow and there was a lot that had to be done in remediation.  

It has lots of examples of case studies (including one with Brandon Turner with a name change) about mistakes made and remedies. 

But that's another story.Has anyone had similar experiences or know of a remedy?

Freitag confirmed, that a Debtor in Texas may be able to force a Bill In Equity, which is a common law remedy that allows for an individual to sell non-exempt assets.

If the sanitary conditions in your unit are such that it attracts pests of any kind, and it becomes necessary for us to undergo remediation in the building, you will be held financially responsible for reasonable costs thereof, paid as additional rent.

Account Closed  you're missing the part where you don't need the legal remedies.  

Some that do testing and remediation may not be on the up and up.

Definitely something you need to remedy, especially since it's likely to get worse over time.