I had to upgrade the waterlines to 3/4 (ripping out the wall, retiling) and replace the drain line with metal pipe, (dig up floor, plumb, concrete, retile).  

This was a 0.88% rule (close to 1% rule = I really dislike that guideline now). 

If a full scope appraisal showing the land value was not completed during the purchase process, taxpayers may consider the following options:Rely on the county tax assessor’s allocation: A taxpayer can review their county tax assessor’s property allocation, which usually provides an assessment of land and improvements based on the county’s guidelines.

My contractor poured a self leveling cement over the current concrete slab.

Please be concrete and elaborate.

This is correct, a lot of the FHA guidelines have changed in the last year making ADU financing a lot more acceptable and easier.

But, it only said that I could be fined and possibly put in jail if, (I act as a real estate professional without following the guidelines and meeting the relevant requirements).

Nothing that is remotely concrete.

@DeAndre Mason If the lender is telling you that you need a 660 to cash out then that would be a lender overlay and not part of VA Guidelines. 

Mortgage, Line of credit,heloc, heloan.Lenders follow their own lending guidelines for investment properties.