Welcome from Colorado.
I don't think we have many members left that remember re-jetting carbs or using different brands of adjustable jetting, you may wait a long time for someone familiar with Thunder products to chime in.
I'm not sure if you've ever brought a 660 to elevation to have experience with what happens and why. In theory what you're going to deal with is an engine top-end that can handle the amount of gas provided with stock carb jets, if the air pump can provide enough O2 to burn the gas.
I'm luckier than most because I can make a carb change, go for a ride and not screw up an entire vacation. I can go back into the garage and make another change and take another quick ride to test the results; visitors to the area may not want to spend their entire vacation testing to then go back home.
When I was changing the carb jets for my area trail conditions/requirements and riding style I learned that when lowering the amount of gas delivered for the O2 available sucked in the performance department for my 660. I don't remember the different jet combinations I tried, maybe I was looking for tooooo much unlike wgc and his recommendation.
I've ridden many miles with wgc and his stuff works for how he likes to ride, so maybe you want to highly consider your trip using his jet recommendation. He's been a member here a long time and I would trust anything he says (except 'We can get to the gas station in Silverton'), he's been there, done that so knows. He was making less than a 3% change in amount of gas delivered, I ended up adding @200% more air by drilling the air box lid.
As for opening/drilling the air box lid for more volume, I did it because a new lid can be had for 22 bucks if I didn't like the results. As the lid is under the seat only dust is ever found on top of the lid. I do carry a roll of tape in the event I need to cover the holes to cross deep water. In your case if you got home and didn't like the holes, epoxy can be used to fill them later. Years ago I calculated the increased opening as compared to the stock snorkel, the holes allowed close to two more times the volume of air, and the stock filter works great to this day.
So you know most dealers back in the day changed the jets before the bike was delivered new to the first buyer, not because it worked but because the dealer could then changer more $$$ for the bike.....it was a profit center for the dealer. Years ago I had a few buddies bought used 660's because of mine and theirs sucked in the performance department, all we had to do was give them a full tune-up and install stock jets then give'm more air.
As for the tire p.s.i., depending on your tires be prepared to experiment for the area you pick. I added taller tires and the added sidewall required me to go up to 11 p.s.i. in the radial tires.