Seattle's real estate market is characterized by high property prices, driven by strong demand and limited housing supply.

There were red flags from the beginning. 

In contract to purchase a CFD in MO. Have done most due diligence items, but I'm stuck on two pieces that I'm not sure about.1. The seller doesn't have the borrower's driver license or any identity verification paperw...

Probably not, because in some states would change the tax status of the property to Secondary which could be a red flag for USDA especially if they are the ones you are making the payments to, which is the case with USDA Direct loans. 

And if they see a huge red flag, then you'll feel ok about ditching the deal.And don't do this again, waiving contingincies is for pros.

Is this a major red flag of her professionalism?

I know sometimes they get characterized and grouped together, but this would be very different with the schedule C and active nature of what I'm planning to do.

The more I'm thinking about this the more red flags I'm thinking of.

During inspections and walk-throughs with professionals the ancient waste sewer line were flagged as an issue because it is very old, probably cast iron or something.

If so, that's  a red flag.