Theoretically you could go no-money down on a VA loan and then still take the money you've saved as a down payment on a commercial property.

On top of that, I will be buying these properties under an LLC, which is notoriously difficult in this area without a larger down payment.

Ps - I don't see your mortgage payment taken out?

Check out Lima One Capital if you don't already know about them. 30yr fully amortized, 25% down payment 8% interest rate range. 

That being said, I don't think a pre payment penalty should be a worry.

My question is I do not accept partial payments and I charge late fees if not paid in full by the 5th.  

It is considered an unsecured loan unless you and your borrower agree that he/she will put something as collateral for the loan re-payment. 

If you have deep pockets or a partner willing to pony up be prepared to outlay 30-40% of the project cost between down payment, closing, first construction draw, etc... while you wait for inspections and draws from the banks to be processed. 

I am trying to get a deal worked out where we will purchase the properties very cheap, sign a contract that gives us 120 days to make a larger payment, and during the 1st 90 days rehab them, then on day 90 pull some equity out of them and use that cash to pay off the wholesaler.

However the math is simple… run an amortization calculator see what the taxes & Mort payment are, and then know what a flat in that area rents for, With that said here is 2 typical examples of Albany propertiesNew Scotland area 2 family’s run around 220k, 6k taxes, 1k insurance payment would be around 1570 a month, typical rentals would be around 1300Washington ave areas 2 family will run around 140, 3500 in taxes, 1k insurance would be about 1000 a month, with rentals being around 1000 a month.So you pretty much can break even in the not as good areas, grab a roommate or 2 and you’re really cash flowing.But don’t forget about the big savings of the low down payment and locked in low interest rate when you plan on exiting in 2-3 years