Some cost that may vary based on location will be your environmental impact study, your list of cost from the Architect may see a lower cost for the schematics on a smaller project, with similar footprints for all four units, versus varying unit size, and scope requirements (less work, lower cost for A&E), the feasibility study, proforma, 3-D renderings, and other associated cost are going to depend on where this project is going to be built. 

I would stay away because since there was a fire it is going to be deemed an unsafe structure attached to it which means architects, engineers involved on top of the permitting process.

I am looking for Architect and GC referrals with experience with full gut rehabs of a 2 flat with the possibility of turning it into a 3 flat, and possible rezoning. 

Pre covid-$175 sq ft for construction for 3 and/or 4 bed/2 full bath 1250 sq ft apt's in a triplex and $25/sq ft for all soft costs-architect, permits, SAC, park fees, landscaping, and various other soft costs ect but not including the cost of a standard sized lot.

The report must be prepared, signed, dated, and sealed by either a New Jersey registered architect or a New Jersey licensed professional engineer."

Also, would I architect be able to design all this or should I reach out to a engineer?

You'll need an architect to prepare the plans and help you prepare and give the presentation to the town for your building permits. 

It's a small world, that's my architect, he did the schematic design.

One is an architect and the other is a GC.

I worked alongside my architect to navigate the process and was awarded a permit.