I've been wanting to get some advice from people about my specific situation, but there's a lot so I'll try to keep it to the point;In short, I'm wanting to "officially" start my real estate investing journey, making it my source of income - and I'm wanting to do house flipping as my strategy, at least initially.  

At the same time, I believe it’s important that we approach this situation calmly and constructively, as we both share the goal of resolving it efficiently and fairly.I did find your email to be pushing and impatient, which I didn’t appreciate.

There is nothing in the original post that stated the resident's situation was anything like yours.  

If you live in the illegal apartment, and it's separate, then what you've done is use an R-1 (single family home) zoning as an R-2 (duplex), and since that wouldn't be legal, the tenant may be able to successfully sue you for renting an illegal unit - even if you are in the illegal apartment - just because it's not legal to have 2 separate apartments on that property.I'm wondering if you could somehow rent it as a roommate situation, though, and get around that.  

The best strategies will be tailored to your specific situation. 

After reading Brian Burke's post about his apartment syndication deal that went terribly wrong, I understand even very successful people can face some pretty challenging situation.

Throw in the fact that properties over the next few years most likely will have very low to zero appreciation and they probably do not get you a net of $6k a month even if you considered the principal payments you are paying down and lending right now is a far better situation to be in than owning property - just as the opposite was several years ago during very low rates and high home appreciation. 

A $200,000 duplex might have identical rents in municipality “A” and municipality “B” but the property tax rates will vary, local regulations will dictate licensing requirements, labor rates will vary & the particular location will dictate insurance premiums since insurance carriers will weigh local replacement costs and whether the municipality is viewed as being a “plaintiff friendly” in arriving at insurance premiums.Better situated assets will attract better tenants.

The slippery slop in both situations is that I would suggest sticking to one thing and not spread yourself too thin.

In that situation I probably would have paid a contract to install an egress window.