Has an architect given you a construction estimate?

They were completely open about it, but it was a prominent wholesaler/attorney who made me throw up in my mouth a couple of times.

I would start with developer or an architect to help layout something. 

You'll then need to have your architect accommodate those requirements.

Generally, an architect should suffice and your city probably requires one for changing a layout.  

If you were designing a building in NYC, which brand name architects would you hire to command the highest price point?

One possible option is to drive light wells in various places (you loose space but gain units) to provide the core units with both some light and alternative egress / exit (fire code in many places).Make sure you have a good architect / designer who knows local code before you go to far.

The estimate came in higher than I expected and I am trying to wrap my head around how accurate the estimate is considering the Architects fees are based on 10% of the total cost of construction.

How much is the architect fees will be?

Adding plumbing and kitchens to an upper floor which only has bedrooms would introduce structural support questions that may need to be addressed by an Engineer or Architect in my area.