Felt like I was in the same boat when I first got here with the inadequate knowledge and money.

We investigate and determine insulation is inadequate in the corner of the room and tell them we'll reduce rent to open the wall and re-insulate (no mold present).

That means part or all of the closing costs are being added to the mortgage.

If they're concerned I'll lose some or all of the account value at the same time as I default on the loan, they could roll the contribution money into an identical account at their institution where the only investment option is cash (or whatever they consider safe enough). 

When the custodian has control of the assets, the resulting fees and transactional delays can add up to a bad experience for the investor.A checkbook IRA or a Solo 401k (if you're eligible) will give you enough control to avoid most or all of the custodial issues.

Did I miss anything important or critical that made my analysis inadequate? 

Keep some or all of the money invested if you like, or use some to purchase investment property again. 

The door doesn't close well or all the way and it looks like there's new damage to the door frame, maybe like someone was slamming it?

Im not to familiar when it comes to windows so I'm not sure how things work or all the different types of windows.

Since you'll be using most or all the money to pay off the original financing (your family's HELOC), it makes sense to get a traditional refi.