Usually this feature of the 401k would be utilized when you have some personal short term financial need and can pay the loan off within few years.

You need to keep one continuous set of books under the legal name of your LLC. 

If I were to focus my business only on VRs and continue to scale with a goal of let’s say 100 units, I’d most certainly build a website.

Now starting to wonder if continuing to rent while investing in an out-of-state market would even be a better option!

But the short answer is there likely is a way to meet you objectives while completing a 1031 exchange which also preserves your option in the future to continue to exchange real estate.  

Ultimately we decided to continue pursuing this deal as the overall numbers are still excellent.

You may want to consider that the interest rates are continuing to creep up, and in 6 months they may be higher than they are now as a result you may want to hold out a bit longer on the refi. make sure that the deal at whatever rate you choose meets your financial objectives just incase you cant refi for whatever reason at the time that you initially projected.   

You can think about putting that into a high interest savings account or maybe an ETF to let it grow a bit, while you achieve 1&2, and continue to save.Your on the right track by asking questions.

Ways to mitigate the risk is to continue strong communication with contractors with weekly status updates.

First, if you "sell it now" and then continue to do the work you put yourselves and your buyer at risk as you will be acting as an unlicensed contractor.