The properties I'd be looking to finance are conventional single family homes and condos with 20-25% down as investments.

The drawback was taking 3 months just to get a conventional investment loan.

You can either refinance with a conventional 30 year fix rate mortgage or doing a HELOC.

Am I able to structure a loan where I just borrow the funds for the repairs (since I should be able to get a conventional loan for the property itself)?

My strategy was to refinance cash out on my current property and put a down payment into a conventional loan for the duplex.

Conventional loans, those that meet Fannie Mae/Freddie Mac rules, are only available for properties titled to an individual. 

I assume you are doing a 30 year fixed 25% down conventional loan. 

If you house hacked and lived in one side and rented the other after 2-3 years if you paid down some more of the equity you would have a better chance of then getting conventional financing and buy out the CFD.

I am not eligible for a conventional loan as I am working for a start-up company and will not be approved for a mortgage.My thinking is to seek owner financing,negotiate mortgage directly with owner, and put up to 50k down for first property.Am I going in the right direction seeking financing directly with owner or do I have any other options in my current position?

Now that I know this, my strategy moving forward has adjusted drastically.From what I understand this rule is enforced on conventional loans depending on the bank and LTV.