Is it worth taking advantage of low interest rates and applying to refinance? 

Use that advantage when the time comes.

They didn't take advantage of it.

I do have some debts I could pay off instead of bringing the down payment higher too.Also I like this house because in 6 months or so I am looking to do a cash out refinance to take advantage of this equity.

The deal is almost in the purchase price.I used to work for institutional asset management and equities and alternative investments do have a place in your investment sphere but for me, real estate has been the only thing that allows me to "not work" when I don't want to.I do also take advantage of solo 401k which allow you to put 50k+ per individual tax deductible every year so I am still heavily invested in the market. 

Zack,Is there a requirement regarding how far away you have to move to take advantage of the second tier entitlement?  

As some of you already know theres many wonderful advantages of owning real estate come tax time.

If the property doesn't meet the VA standards, then you won't be able to use VA and will have to pivot to a much less advantageous loan product like a commercial, etc. 

Maybe you can pre-book placements for a discount to see if some will take advantage of that option.

I would then rekey, fix what needs to be fixed, and market the unit.I would also get in touch with her and let her know I'll be marketing the unit, since she has moved out and that is to both our advantages.