The costs to hire a structural engineer and then remediate the problem was far greater than I was willing to spend for a buy and hold.

They intercept them at the search engine level and then they sell the "lead" to you.  

I recently graduated college and started my career as a mechanical engineer and have recently decided that while I love my job I don't want to work for the rest of my life, and real estate investing makes the most sense to me in order to gain financial freedom before I turn 60.I have been reading a ton of real estate books and discovered the bigger pockets book on rental property investing which gave me a great introduction to all the topics and possibilities in real estate.

Standard 203(k) Financeable Repair and Improvement Costs and Fees The following repair and improvement costs and fees may be financed:  costs of construction, repairs and rehabilitation;  architectural/engineering professional fees;  the 203(k) Consultant fee subject to the limits in the 203(k) Consultant Fee Schedule section;  inspection fees performed during the construction period, provided the fees are reasonable and customary for the area;  title update fees;  permits; and  a Feasibility Study, when necessary to determine if the rehabilitation is feasible. 

I have put it under the carpets for now and when I redo bathroom and kitchen floors, I will put it in the traffic areas under new tile floors or maybe engineered wood..not sure yet.  

Currently, we've decided to split the cost of a new septic system and still waiting for engineering plans to come back.

I also don't recall seeing such a high alteration fee, or one based on the percentage of the renovation budget (It doesn't cost more for the condo's architect/engineer to review more expensive fixtures/finishes).

A structural engineer would be your best bet to have a look. 

My firm does engineered cost segregation which requires Form 3115 if the subject property was purchased prior to the current year, called a "look-back study".

I am studying to become a Software Engineer (and hopefully someday design software for REIs).