If they foreclose and take a loss, they are entitled to come after you for a deficiency

We did put in the CC&R's a penalty if they were not adhered to, which was the HOA could correct the deficiency and lien the property for the cost.

Are there any other easy affordable measures I can take to offset the documented deficiencies that have set building codes in many cities against it? 

The answer is most any market near colleges that have student housing deficiencies, I have several client that employ this strategy near UCF and are pretty successful.

The Home Inspector report revealed major deficiencies in the rehab and the Home Inspector told me that the rehab was like “putting lipstick on a pig”.

The most effective strategy will be sold comps and any evidence you can provide of deficiencies in your property (pics that show it's outdated, or in disrepair).

The city will inspect on occasion but they give you ample time to correct deficiencies before re-inspection.

If there is one area that I was deficient in (and there is more than one), is construction/M&E for both residential and commercial. 

Namely,"If the wood infestation report reveals the presence or indication of or damages by termite infestation or other wood destroyingorganisms, Seller shall remedy such deficiencies and shall furnish the Buyer with a CL100 wood infestation report"and "If the Seller does not make the repairs and treatment, the Buyer shall have the option to(1) accept the Property in its present condition, (2) negotiate with the Seller for the payment of these repairs and treatment, or(3) terminate this Contract by Delivering Notice of Termination to the Seller."

First - leave your emotions at home, NO COMPLIMENTS of the property, look for Value Deficiencies !