I would opt for somethingHard to quantify in terms of pricePurely in the "gift zone"For example, if you give them a $50 gift card there is a very real human tendency to compare the dollar value to what you perceive the discomfort to have been worth, and most years, and ESPECIALLY this year, you don't want anyone's lizard brain doing that calculation.Something like a bottle of wine and a doggie-pampering gift basket accompanied by a note expressing something like "I am thankful for you and apologize for the inconvenience you experiences around this roofing fiasco. 

Specifically regarding Shampoo/Conditioner - do you refill each visit so the bottles are always full, or replace with a fresh each time (seems expensive)Are you going to a grocery store to buy salt, spices etc?

You can wear a mask and give them a bottle of lysol when you leave.Then consider what needs to be fixed, likely its a lot more than you think as otherwise he would not be making $40k. 

I wouldn’t buy a bottle of water from this agent.

He said the couple continues to find more bottles.

I assumed there would be a bottle of whiskey or six pack of beer under it.

going to be crazy back up and bottle neck? 

Don’t get rid of upper cabinets - open shelving is not a better option in a kitchen, because there is no place to hide the mess of boxes, bottles, bags, etc, which are not visually flattering.  

Hand written note with a bottle of bubbly on ice waiting for you.

another option would be to use a diamond blade on the grinder and to cut out the affected area. use a spray bottle filled with water to spray the blade while in operation in order to minimize the dust. two bags of concrete mix may be sufficient to fill the void.