During inspection noticed cracks in the driveways and after further investigating found roots causing the cracks and were going into foundation..My main concern was roots damaging pipes before having that issue I had tree removed.Honestly I have no idea how big are Cherry Trees and how are the roots.

You have the red flag already...."

There are many red flag involved in your initial post.

My future is real estate flipping houses to pay for rentals multifamily is the path I want to take (4 green houses trade in for 1 red hotel).

The electrical panel will have a red placard on it. 

I ended up going to get ALL the material, hot and cold(Red/Blue) and we ran it ALL brand new PEX.

He needs to run a camera in the sewer clean-outs and check for bellies and roots and separations.

That would also be a red flag to me. 

If the contractor is unfamiliar or uncomfortable providing you with a fixed price quote ... should this be a big red flag about the contractor?

@Bethany Rankin being rejected for a reverse mortgage is a red flag for you then it could mean a number of different things1.