@Nate Bulkowski - If you go the route of 1031 and have have difficulties completing the 1031 exchange on the capital gain portion, consider opportunity zone investments.

Do I care about the extra interest that will not accumulate or do I care less because I can acquire another property and someone else is paying the interest?   

If you have extra money to give away, I guarantee I can find charities that are in greater need than your tenants.I also disagree with small increases over multiple years or even over a one-year period.

meet with a lender and go thru the formal pre approval steps to know for sure ..if the 15 yr fixed payments dont work for approval - fall back on using 30 yr payments ( and then just pay extra to payoff the loan quicker)  

Finding a good contractor was difficult. I

In addition, should I pay the extra 600 to bring the rate down to 4.99%?  

Rents should try to reflect any extra costs you incur so long as the rent remains in line with the market rate.

It should be mentioned we will still be nearly doubling our investment with the prices she is suggesting, but could potentially be missing out on almost an extra 100k in profit should we finish and list at what I think it feel the market would support.  

oh also - if you are going to allow pets, especially dogs, get extra cash for them. 

So if you need extra money LOC is an open option.