We have found that a change in our procedure has prevented alot of these problems.

I truly do anything I can to prevent taking money from her in the deal.

Or are there provisions that prevent a buyer from doing so?

You would likely need to talk to an attorney and ask about how that would work since you might be in a bind waiting for the tenants option to expire and be prevented from doing anything until that time. 

That construction agreement may not be valid without a license.Forget any construction financing, you can't give the property as collateral.If suppliers extend credit for materials, they will generally want the address and owner to sign or a licensed contractor with a valid construction agreement allowing liens to be created.You can file your option and cloud title, but that cloud doesn't prevent an owner from selling the property subject to that option, the new owner will be obligated to sell it under the option, but if you fail to exercise it as agreed, they will own the place.

Regardless of the price range you're working in on the retail (agent side of the deal), it doesn't prevent you from investing in homes in any price range.

Here is one that might seem obvious, but can really prevent many headaches later. 

Estoppel is a legal doctrine that prevents a person from asserting rights or facts that are inconsistent with earlier actions or statements.

If you can be certain to find a line between rows of nails, you could set your circular saw to (a shy)1/4"and cut a trench to allow you to get under the floor and pull it up.Around here it is very common in old houses (Second Empire, Queen Anne, etc) to have accumulated 3-4 layers of flooring over the years  - we renovated one two summers ago which had an original pine floor over the subfloor; two layers of hardwood above that and, in places, a layer of asphalt tile on top of the hardwood.  

so how do I prevent from making the mistake of low balling the repairs to much?