We actually transferred funds to our checking, and wrote checks out of that.

Transfer some paper assets into real estate holdings and/or create cash flow. 

In general contributions into an entity do not trigger a taxable event.Doing it prior to sale leaves you open to issues of intent and holding period and the thought that you're somehow hiding gain somewhere in the entity transfer.  

We called the title company first thing and found out the transfer won't happen until 4pm.

Actual transfers of property are recorded in each county registry of deeds, normally the day of closing, or the day after. 

Also what method do you use to transfer funds from your property LLC's to your 'main' LLC, do you just call it a management fee and bill the child LLC's?

My cousin keeps mentioning the "look back" regulation that requires transferred assets to be held for 7 years before he could liquidate them without the state "taking" everything.  

You don't really need to do that yet as you can get the traditional financing in your name and transfer title into your LLC if you have one.  

They should have conveyed to you the conditions of the lease and that it remains in effect through the transfer of ownership.

And you can eventually transfer them to an LLC if needed.If flip with hard money, then it would be okay to do an LLC.