Who should pay for these changes: the architect or me?

Degennaro Contrating (John Michael Degennaro)Bill Lake Modular Superior Walls Foundation Doug Cutler Architects

If you are in Chicago proper, then start with an architect like @Samuel Pavlovcik. 

Permits are around 20-25% of construction costs in Oakland and you'll need drawings - which could be another $8-15k for a professional architect and engineers.

I think the first step for you is to consult with an experienced architect like @Samuel Pavlovcik and then a reputable contractor such as @Jonathan Klemm.

We worked with engineers and architects to complete the design phase alone and combination of a General Contractor who pulled the permit for us, our subcontractors, and our in house renovation and maintenance team to complete the work.

From there I can obviously back out equity and financing fees and figure out what I can pay for the land... that's my goal at the moment.Looking for some insight on how to better estimate construction costs as well as an architect that would fit this project size and maybe any suggested financing structure aside from bank construction loans, which are extremely hard to come by these days. 

Best to find a local Architect. 

There are multiple books on amazon about estimating rehabs - but from your questions, it's probably best to start talking to an architect about what is even possible.

By the way I was a SW engineer in San Diego (a JSF architect), that house hacked my first house (but it was a SFH, not 2 units).