As a Professional Chef i am naturally handy with my hands.

Don't forget to subtract selling costs, transfer tax, and interest payments to arrive at your "true" profit.

I have been reading everything I can get my hands on for the last year and have a decent cushion to pursue my next property with the goal of 15-20 cash flow properties. 

Buy a hand steamer for all baseboards and gaps.

Is it ok for me to transfer money from the llc to the personal checking?

Going around the attorney to the seller through the agent to see if he'll play ball with you forces his hand.

If you decide to move those funds into self-directed IRA as @Amanda Gust suggested - there will be no tax or penalties associated with the transfer since it is be considered Direct Rollover.

If you're handed the keys to the landlord then you've legally transferred possession.

With SDE @ approximately 25% of revenue, I am inclined to pay roughly 1x revenue/4x earnings for this business, would love any opinions otherwise.On the other hand, the idea of growing organically is very appealing.

Yes, and same with the property, the buyer can cloud title and tie up the transfer of title, thus tying up the sale of the property too should a seller try to take a deposit under bad faith.