I have seen stuff during demo that you look at the rot and ask yourself, "how is that still even standing".

However, the inspector wasn’t aware of the interior leak, as it had been dry for quite some time prior to the inspection.

If there are gutter issues, dry rot, water damage, it can go hither.Piers in the basement are not that big of a deal, figure $350 per pier. 

I am hesitant to wait until I can do a 3.5% down payment without running me dry, but I don't want to miss out on potential appreciation \ cash flow opportunity.

So I contact the Twp and come up with the solution that I (Meaning my renovation company) will fix the rotted beam(which is what was causing the structure to be unsafe) as long as the bank reimbursed me at closing for work done.

Log replacement can be very expensive if they ever rot and very few people do it anymore.

The only thing new in the world is the history you do not know (according to President Harry Truman).(1) deflation: During The Great Depression (1930s) and The Great Recession (late 2000s), lenders went out of business and money dried up.

FR porch (rubber membrane rotted) , Main roof (rodent chewed a large hole through it) and RR roof (3- layers of shingles) need replaced (~$15k)2.

Today we cut out all the drywall and removed the flooring so it could dry out and not grow mold.  

If you are trying to do a finished basement you'd be better off getting a contractor in to do some additional drainage as well to keep it as dry as possible.