I'd consult with your lender for the specifics of how the funds should be transferred from your family to you.

They did offer to allow him to transfer the deed back into his name and keep the loan, however due to his circumstances that is not possible.

@Glenn PaulsonI agree with @Will Barnard instead of cashing out your IRA and being subject to an early distribution fee, and higher income taxes, you could transfer those funds into a self-directed IRA and purchase the property in the name of your IRA.

Again my questions is, should I be concerned about the current landloard transferring these funds to me?

I know the next thing would be to do a QuitClaim to transfer the investment properties to the LLC. 

These are things you can give in detail to the buyer:Cash flow on businesses, condition of equipment, payroll, more info on liquor license transfer, are there existing liabilities, is the seller willing to sign a non-compete clause in case they want to open another similar establishment or invest in one,  ask about current manager...staff experience, are they willing to stay. 

If I put down 50% and he puts down 50%, where and how do the funds join together and get transferred for the purchase.Once the house is purchased, what costs must be taken into account?

The prior owner's certificates do not transfer to you.

Or are they transferring larger sums from other retirement accounts to get going?

Are there any legal/financial ramifications if I collect rent through my personal Venmo account, then transfer to my business account for my rental property?