We conduct Phase I ESAs during due diligence which are supposed to uncover these.

Then, I would add a contingency for any necessary foundation repairs uncovered during due diligence shall not exceed an estimated 10k (or whatever number you arrive at that still meets your criteria).  

I have a question about Buy and Hold strategy that I was hoping some of you could give your input on and perhaps point out the flaws in.I feel like I keep running into properties that have been flipped recently and look very nice/completely re-done, however they are in horrible areas still.

With that I think you are evaluating a single family in a flawed manner as far as applying a cap rate to a single family rental.

The tech came in on Sunday 1/29 at 7 am as she couldn't make Sat, and uncovered that one of the parts needed to be replaced but suppliers are closed on Sunday, so he couldn't get it that day.

Is my logic flawed?

There is also extensive drywall damage (including some visible mold in one small area) due to roof leaks, some which my inspector feels are active leaks, and a septic water level warning light.I was told by the management company that an OO doesn't have an inspection period (not true) and that HUD will never do any repairs (per their handbook they can repair major--roof, electrical, plumbing, structural, septic--issues at their discretion if previously undisclosed but uncovered by OO's professional inspector and reported to HUD within 15 days, don't know about in practice). 

I only advise to buy if the cash flow is very good and never plan or incorporate appreciation into profit equations so my motto is patience then pounce as you have to be ready and move very fast when you uncover the one you want.

I'm sure more research on that area would uncover the difference.  

I always thought the concept of HOA's are incredibly flawed.