It's going to take longer than you think, with more red tape.

It is a mess and you are partly to blame because you are ignoring all these red flags.Write her a notice that says the home is uninhabitable due to the water leaks and you are terminating her rental agreement, period.

They don't have the red tape and seasoning conventional loans require.

I don't know about commercial loans, but some hard money lenders offer products that allow a flipper to refinance  or do a cash out without all the red tape and seasoning.

Is there any red flag?

A nuclear facility was built including the nuclear tower. 

go easy on me, I'm color blind and a terrible artist...heres what I put together...Rough sketch with the walls i want to remove in red, existing/walls I'm keeping in yellowhttps://drive.google.com/file/d/1h9Zsm8YeuIYLlbInY...Rough sketch overlay to aerial photo to show hip roof. https://drive.google.com/file/d/1OK90I7ikqJp6_7b7a...Attic shot looking west from the corner. 

I am looking for something more strategic to were I can set targets, milestones for projects, properties, and my company and track and manage their progress.

Worst case is all hose red flags are significant and something is amiss.

I would see that as a big fat red flag