If you have an active root...over time it will grow back in there unless you excavate, cut and remove. 

So can I calculate my cash on cash return like below $40K(appreciation)/($42k(Down payment)+(2.1K(Monthly payment for Mortgage+HOA)*36)) = 40/(42+75.6)= 34% so the annual cash on cash return is about 1.34 to find the cubit root.

Can anyone recommend good companies to root cause  and implement solution to fix this issue?

I would say on a rental property that's unrealistic, if it really is an issue on a property, better to address the root cause.

I guess I can't wrap my head around the fact that anyone can make an argument as to how the doors and windows being left open was not the root cause of this issue.

Generally no because the root system is still in place.

we changed the driveway because of the cracked cements of driveway cause by the tree roots.

Some old Milwaukee sewer laterals have tree roots that like catch on to stuff.We also eliminate garbage disposals during rehab and normally we have someone from our team check out issues, before we send a plumber.

For me, my focus is going to be to go back to my roots and flip a couple of properties to generate cash flow.

I rarely see anyone address the underlying root cause of the issue.