If you have suspicions because of the hill, pay an engineer a few hundred dollars for an inspection of its condition. 

I am 25 yrs old and have been a software engineer for the past 2 years.  

If your car engine  is 2% efficient... 

Our property had shown signs of termite damage to a structural beam during the initial inspection, and I paid for both a structural engineer (to verify the beam’s integrity was sound) and a termite inspector (to verify there was no active infestation).  

My insurance got involved n November 2017 and said since its a 'Walls In' policy and the HOA are responsible for the issue and the damp inside, the claim ought  to be with the HOA's insurance policy (i also pay for that via dues)An engineers report requested in December and was finally provided to me in February 2018 , and sent to the HOA in  February 2018 with an explanation.After a lot of avoidance and misdirection and wasted time (with the damp increasing) the HOA admitted that their policy was no good and so they need to compensate me direct.

I met with the structural engineer today and he believes that it just needs a few lally columns and an lvl to fix the problem, other than that it has been fully renovated.

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.