Negotiated it by having a strong offer to set us apart.

Once you have discovered YOUR Why to get involved in REI, then you can establish your goals and set your investing criteria.  

I am taking it upon myself to set a more strict personal budget as well as creating a business plan.

Call your local Sheriff to ask how they set the Initial Bid Price. 

If we are not longer able to give rent credits, then does that extra $500 a month get applied to closing costs or the price of the home up front when you first set up the price to sell? 

I set a low anchor price and worked from there.

But seeing the value increase by this much also reminded me to trust my intuition.

You're immediately setting yourself apart from all the real estate agents out there who think they know how to valuate real estate by replacing square feet (and price per square foot) with features of house, which may mean the appraiser takes your analysis more seriously. 

She must charge you the minimum AFR (set by US Treasury).

When i was rehabbing properties full time (2011-2014), I also always aimed to set my re-sale price 5% shy of market price.