Do not pass go, go straight to jail and pay the $14,000 fine.....plus whatever civil costs arise. 

Now that it is, I'm curious why there doesn't seem to be any pushback, revolt, or litigation challenging it.

I would not place San Diego on a listed with difficult permits or inspectors (but have encountered some arrogant ones who seem to like the power they yield but I figure it is because they have a civil servant job that will not pay significant dividends until they retire in city pension. 

Because people fall in love with returns and do not ask how is that possible…Of course investigation is ongoing but this is all alleged.https://www.sec.gov/enforcement-litigation/litigation-releases/lr-26076

Whether it is litigation or surveillance I would do whatever it takes to protect yourself and your investment 

A civil engineer may be able to help or point you in the right direction.

Contrary to what you may hear, I do believe that you should have properties in LLCs, for reasons I won't get into here, but let's say I sleep well at night having full first-hand knowledge of litigation procedures and knowing that if my real estate endeavors fail, it won't be due to collapse from liability.

At least according to the SEC : https://www.sec.gov/litigation...

An Architect can look out for your best interest in the project plus can bring all the Engineers necessary for the build (Civil, Structural, MEP, Sprinkler/Fire suppression, etc.)As far as the build itself, if it's in an established city or town on a tax lot, then you'll need to go through the design and permitting process, gain zoning approval if necessary, and then build up from there.

I would caution that any outstanding litigation or taxes would follow the LLC if something went unreported or paid.