Long story short, I have 3 properties in my own personal name: Small multi-family properties (a 4 unit and detached garage bank, another 4 unit, and a 3 unit) that I had residential HELOCs on in the second position, with a fixed residential in the first position. 

I have the option of pulling out a HELOC from my home in KY that could cover the amount for both HVAC systems. and if i do that i could most likely use the cash flow from when i move out to make the payments on the HELOC.

Have you looked in to getting a heloc on your primary home?

I've considered taking a HELOC to do repairs but after reading Rich Dad, Poor Dad, I've second guessed that idea but leaving as is would negatively impact selling the home.

Personally, I would only use HELOC money if the project will be rather quick.

You do not own the home so you cannot use its equity instead you are borrowing money based off of the current owners sale price.Using the same banks/lenders Heloc in some cases can be fine since its attached to another home.

I'm considering turning it into a separate apartment and would really appreciate any suggestions or advice on how to make that happen.Lastly, I have been researching HELOCs for possible use as a downpayment for a separate multi-family home.

I was asked the same question when I was applying for my HELOC, and I was approved with no problems.

Required repairs for federal lending approval are generally more easy to include.We've seen folks with helocs attached to the property who have accessed the heloc to repair the property right before the sale since the heloc has to be paid off as part of the sale. 

In many cases the HELOC would make sense because it allows you to hold on to that rate.