There are a bunch of non-intuitive measurements that banks care about.

Both the SE and myself (also an engineer) are pretty certain that foundation issues are within the $25k range to remediate (probably in the $15k range - due to the localization of the issue), but the lenders don't want to lend on "ifs" and "maybes" which I get completely.I think my next step, is to see if I can get the seller to let me dig up along the problem wall, get the SE back out so he can say for sure, it's fixable, in x price range.The one thing I'm concerned about is that I'm too close to the deal, and I'm getting attached to the numbers, but intuitively, it's a risk I'm willing to take.

I took the loan to avoid penalties and taxes in the first place so incurring them now would be counter-intuitive.

It's really intuitive and easy to use - I was looking for something that I wouldn't have to struggle trying to figure out.

Looking back, I suppose I knew this intuitively because I really do care that my properties match what the market is looking for.

I would be skeptical that $50 less per month will keep someone in a unit an additional 2 years, so it seems that staying at market rents makes sense.However, if it takes you 2 mths to fill a unit at market, and the $50 savings can cut this to 1 mth and extend the tenancy from 2 yrs to 3 yrs, then you come out ahead by .5% per year on the net return.Likewise, if you raise rents to $50 above market and it reduces avg tenancy to 1 year, you're hosed.Mostly this is intuitive, of course, just the degree of the numbers I was interested in.

I have heard that this type of approach is counter-intuitive for RE agents. 

Doing our do diligence and following our intuition really paid off with that deal.

I know counter intuitive..

Seems counter-intuitive, but it's how credit scores work.