Hopefully everyone can learn from my experience and be better prepared for issues that can arise.

It's possible to compensate for on taxes (not economically, though), but it requires a tax professional.Additional complications will arise if the sale was reported by your tittle company 100% under one of your SSNs, as opposed to 50/50.

But the equity we're holding in those 2 properties is nice, and allows me to tap it with a HELOC when an opportunity arises.

Be very careful of bad faith tenants and "unlawful ouster" that arises in 504B.365 Subd. 5, 504B.231, and penalties in 504B.225 which include "reasonable attorney fees." 

If you ever set up a website where you take your own secure payments, etc and are sure that no dispute will arise with guests, insurance, security deposits (which you have to hold in escrow accounts technically)... go for it.

My question is if I need the initial investment money back what tax implications or other issues might arise from repaying myself.

Great option in a rising rate market. 

I find as you take on renovations, more and more problems arise with older housing.

I started my investing 7-8 years into a rising market in 1983.

Change orders during construction is very common because in many instances things that were not accounted for in the original scope do pop up and when you start opening walls, demoing, etc many surprises can arise.