My question is the following, if I buy an investment property (while continuing to rent where I live), does that prevent me from qualifying for an FHA loan later on when looking to own my primary residence?

The loan may prevent them from getting future loans, especially another mortgageIf you default on the loan and the property is foreclosed their credit will be wrecked.There is nothing short of suing you that they can do if you do wreck their credit.  

@Ken Nyczaj to save you some further headaches and quickly identify your water leak source, I'd suggest having your builder, or you, get a simple water pump and 50-100 ft garden hose (link: WATER PUMP) which will pull the standing water out of the area, and put a carpet fan (link: LIGHT DUTY or HEAVY DUTY) down there for a few days to dry everything out (especially your wood framing and the insulation) to prevent any further/potential mold growth.

This includes renovating (to the level of the neighborhood) and making sometimes significant improvements to prevent issues.

The concern is that there may be some technicalities within the PM side that might prevent us from doing this, so that’s where I need your help!

You'll prevent yourself from making knucklehead mistakes this way.

What I've noticed helps prevent them are 1.

The main thing is not to use the HELOC for long term funds because you don't want to continue paying the interest on it if you can prevent it.

What they learned and how they prevent them from happening again.

But if you do hire, we will do a better job and prevent errors.