When I'm wearing my Architect's hat, I find this to be one of the top 5 "oooops...I didn't think about that" items when doing rehab.  

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?

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

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.

It probably won't do any good but I have written members of Congress, the Senate and the architects of the bailout plan because I think as long as there is talk of a potential bailout, banks are less likely to modify loans, approve short sales, etc.

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

Has an architect given you a construction estimate?

Managing civil engineers, architects, lenders, raising equity, etc. are all major parts of the development process.