I am looking to invest in a duplex or triplex. Which is a wiser decision: Pull money from my retirement account or use the equity from my principle residence? 

If your not savy with complicated multi layered entity structuring, than don't try to do business like you are, and K.I.S.S.

If it is possible for you could start on a multi family home that is easier to get financing including the renovation but you have to live there one year but your tenant(s) could pay the rent that would probably pay enough to cover most if not all of your mortgage payment.It can work well to be a good investment if you keep it for longer term.  

What are the rules regarding how quickly I would have to occupy an owner occupancy multi family home The triplex that I am looking at is fully occupied until end of January 2017

Other questions we have concern things such as finding a good group of contractors to work with, and how to best protect all parties in our transactions, most certainly protecting our family as the top concern.

I plan on 1031 exchanging this house to a 6-10 unit multi.  

My long term goal is to own a multi family property.

The attorney's office will then order a title search from a third party title company that offers title insurance.

I am currently assessing a deal on 3 multi family homes (2 dup, 1 tri) listed for $55k, $65K and $65K, respectively. 

A lot of lenders may tell you the appraisal is free however its not free if you dont close you will still pay for the appraisal typically (its only free and credited back at the end or at the closing table).The other part is to make sure rates are where you want them to be (low enough).