Both units are separated by a fence but share the same address and utilities.My question is can I separate addresses and utilities and sell the second unit (1350 sq ft) as a Single family home? 

If so, then you're more emotional that he did it without permission.

Then, open home depot site  and find out how much materials will cost.it will be a good practice.Last part will be collecting separate bids, and before you do that decide what needs to be done in specifics, like how many recess lights you will need...If you spend some time, it will be very helpful.

How do we get a second loan together or separately? 

You could...but it's probably more beneficial to get a separate loan on that triplex....unless you are thinking it would help you in some way that we aren't thinking of?  

It was filled with old clothes and items and had 3 separate ceilings.

I currently own three separate multi family properties and I’m looking to syndicate my next purchase with investors but would like to understand the best effective syndication model that has worked for others with investing in 20 to 40 unit properties.

I remember being this way and I would get so emotionally invested in a deal... now I just get quotes and make sure that a worst case scenario won't sink the ship. 

As an investor yourself, you know how to run numbers, have a network of rockstar lenders/contractors/PMs, know how to negotiate with sellers, know what to look for in an investment property vs retail, know what neighborhoods other investors are active in and have potential upside, and understand the emotional side of investing as opposed to retail. 

If you are getting emotional just don't answer and cool off.