As far as permits go what about them would you say is the most complicated? 

I might just be making a complicated way to bird-dog.

That may complicate the deal.

So, we are leaning towards buying the property via two LLCs, although I'm a little concerned that this will make things (like obtaining loans) more complicated for us in the future.

This might sounds complicated but your attorney (probate or family planning  better) or a financial advisor can advise better on this because it varies between states.

When you rent out your primary residence, your taxes become "complicated." 

As a data point for you, I underwrote and negotiated a 5 home subdivision in San Marcos last year (that I didn't end up moving forward with because of utility complications) that had a $800k land cost.The problem in this case is the land cost is too high for scraping and building. 

In general the powderkeg that exists here is that your PM has a VERY complicated operation, created by the way they are structuring the business. 

The thing is that my relationship is a little complicated now but I hope it to get back to normal so I am not sure for how long am I going to stay in that condo.

In reality it’s more complicated than that.