However I have been going through as much of the literature and beginners guides as possible in preparation of my first deal (analysis paralysis).

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Also structure has to be a concern.   

As a beginner, I feel, as I'm sure many other newbies do, that the great wealth of information can seem overwhelming at times.

The use of a particular type of deed typically raises concerns for a buyer because of what a prior owner is guaranteeing or agreeing to assist with or not, but like Greg said, if you have a title insurer willing to insure yours it's because they've done their research. 

The main area of concern is how lines 20-26g on the 4797 don't seem to have any provision for the deferred gain that is the whole point of the exchange, so when filled out it seems to show the whole gain as taxable capital gains.  

I really don't understand what my broker is so concerned about. 

Overall I’m more concerned with cash flow and returns than a cap rate but I want to make sure Im creating an accurate and somewhat conservative scenario.

But he may be right as well. you should have gotten multiple bids before you started the project. that would have addressed your concerns regarding overpaying.

Secondly, he went on to mention it cost him $300 to heat 2 rooms for one month over this winter, his concern was the insulation.