Site development, is custom, grading, soil prep...the list goes on.

If you market can bear it, okay.. 

I was wondering if there's anything I can do at this point or whether there's just a risk with this and I'm going to have to bear the loss?

I agree in an open market, buyers will pay a total of what the market bears and if they are paying their agent their offer will represent this.  

Those are net rates (what you pay in payroll), by the time you add taxes and work comp, they are 40% more, then you add whatever your contractor's profit typically 20-35% on small jobs (bear in mind, if client doesn't know what they want, you need to raise profit for the extra cushion when they say "I don't like it"), the reality of that 20-35% is 15-20%.

Im buying a duplex in KCMO and getting ready to move there. this might turn into a long question but bear with me.Its become clear through my research that there are 2 major types of investors out there.

Your contract has no bearing on the tenant's rights.

So with a security deposit, I know I need to put it in an interest bearing account.

Soil?  

Books, programs, and videos can help you get your bearings and build a pretty strong understanding of what makes a good deal and what doesn't.