Protect your asset.As @Ali Radoncic mentions, foundation issues are common. 

I believe that is the baseline goal for every investor.I've been scraping over Google and this forum for a post/thread or an article on an, “investor’s depth in their ability to buy” (Best way I can describe it).

Identify your goals - Figure out if steady rental income or maximizing long-term property value is your top priority.

It's our goal now to start purchasing additional buy and hold properties, but still consider ourselves newbies when it comes to investing. 

Is it common to withhold retention from the general contractor payments until lean release is obtained from the sub performing the work?  

There are a few things you need to look at and take into account.Everyone's financial situation, risk of appetite and goals are different.

Is that the end goal?

It is common that sometime floodplain maps are not always up-to-date based on current conditions, and thus you site may actually be above the floodplain elevation. 

so i am coming around to your way of looking at it. these problems are very common actually (HVAC stolen/roof issue in midwest).

It will be beneficial for achieving your real estate goals.