The reason is most lenders won't touch them because of their source of lending money from the government.

We're looking to buy in the Charlotte area of North Carolina if that makes a difference.Also, although we have owned homes technically we have never financed a home before, so I'm also unclear on whether we may qualify for any FHA programs since we do want to finance this time around.

I'm an asset manager handling roughly 150-170 properties nationwide through the Fannie multifamily loan programs.

Expect some mistakes and redo's along the way to add to the time.Expect any government inspections to add to the time.If you can keep the same team all the way through by the time they get several units under their belts they may be able to go faster--providing they can get the materials.In my opinion, it's more intuitive to look at each unit as a separate job, vs demo all kitchens and tubs in X units as a job.They can still come and demo several units, just for me it's seems easier to keep the Tiger by the tail this way.If you buy all of the materials at once, you will have to guard them against theft and store them somewhere. 95 toilets going missing probably won't tank your budget, but it might tank you enthusiasm for a while.Make sure to budget for a dumpster if you need one, and porta-potties for the workers to keep them from using the ones in the units. 

With-in 2-3 miles we have 2 big university with around 75000 students combined. 70-75% jobs are related to either university or various government departments.

What programs do you have in place to keep residents happy?

Search FHA first time homebuyer programs.

My biggest concern is with affording the down payment combined with any closing costs or fees that come along the way.I've been speaking to a few different loan officers, and the consensus seems to be that conventional loan programs for a duplex property type require at least 15% down. 

I would also look into homeready loans or the bank of america grant program, they might be better than the FHA route.https://singlefamily.fanniemae...https://www.bankofamerica.com/...Not sure if that helps at all, happy house hacking!

These are just a few, there is a myriad of programs out there, just need to write down what you want and expect a program to do for you, then take it from there!