There are often hidden costs--such as: engineer certification of the structure (depending on what the city requires) smoke damage to portions of the unit(s) that are "not affected" additional insurance during the rebuild, sealing the framing that has smoke, etc. 

If I ever got a house without HWs, I would probably go with engineered HW or LVP (wood look).

What sort of fees can I expect for the other stuff (architect, engineer, permits, etc)? 

From what you said the special structural and civil engineering is what's killing your build cost.Lumber has gone up quite a bit bc a lot of them come in from Canada.

Side-skirting booking engines from the big players like Travelclick and Synxis would be a huge money saver.  

If you look at construction world for bigger projects, one of the buzz words is "value engineering."

It's already the 4th geekiest city in the country with all of the smart people working for NASA & the private sector engineers servicing NASA. 

I once reverse engineered my goals and realized traditional saving 20% down and purchasing was not going to cut it...at least at the pace I wanted (and frankly and probably not at all). 

DH is a network engineer and I have worked in ministry/non profit settings as well as customer service settings. 

I'm an engineer, trained and licensed so that lets me kind of 'lean' in to the more challenging projects.