Then a few months later when I have the property in contract to sell my title company turns up an open mortgage. 

I am now under contract to purchase a triplex using my VA loan with a tehab component, where will will live in a great home in one of the most desirable neighborhoods around, while renting out the two units in back. 

I think there are few different ways to do this (e.g: lease option, subject to, land contract) Check out this article to get started then search the individual tactics in the BP search bar to get more info. https://www.biggerpockets.com/renewsblog/2011/07/20/seller-financing-3-kinds/

In the future I will have it spelled out in the contract the lessee agrees to take lien position behind any and all lenders. 

I would recommend doing a contract purchase for the exact loan amount for a year before going with a loan from a bank - if you don’t then the bank will only loan you money for exact purchase price of the house (assuming it’s lower than the appraisal value).

Building codes and permits are primarily a city function, with some input from county level on certain subjects, such as Septic Systems.Primary contract will be in the Planning & Zoning Function of the local city.  

You have placed a property under contract to purchase and are selling your rights in that contract. 

The other option I looked at was GroundFloor which I found in the bigger pockets directory here for crowd funding, however I believe the interest rate will be high since this is a 0 exp flip.However, my father has been running a contracting business for a very long time and he will be my main resource when flipping these first few when it comes to the rehab portion.

I'm going under contract for my first duplex tomorrow. 

Contracts and attornies handle this type of thing, it is exactly why they are used.