If you've repaired all of the major discrepancies can you still get a tenant in there and receive cash flow?

Maybe the investor found a hidden discrepancy. 

Let’s start with the math.Purchase price: $760,000Conventional loan limit for area: 647,000I was looking to put down 5% of purchase price: 38,000This leaves me with a discrepancy of $75,000.This will be a house hack with incredible upside potential and appreciation.

It also meets and exceeds all of our check boxes.I can only put 5% down comfortably.With 5% down and a loan limit of 647,000, I have a discrepancy of $75,000.

The city building department came back saying that there's a discrepancy with our property lines and are holding our remodel permit plans until its sorted out. 

Maybe you've already done this but  I would print out a set of the plans. schedule a meeting with the decision makers. show them the discrepancies.

Take a look at this real example I got today.Thats a HUGE discrepancy between what I have it set at. 

You're better off from this rate discrepancy, as a rule.Complication 2: It gets really complex real quick if your numbers are in reverse: $40k gain and $50k loss.

I agree with the other comments that you should also shop around to find other lenders and also take a look at their underwriting to see if there are any discrepancies.

Address discrepancies, different SSN's showing up on the credit report, etc.