I've done the LA-SF trip on my F6B maybe a dozen times over the last few years. The stock seat has been just fine for me, but the biggest difference was installing the Madstad. Of all the mods you've listed, this has got to be head and shoulders the best investment. It made wind noise negligible below 80 mph.

I don't have highway pegs, never felt the need.

I would never rely on riding jeans for protection at interstate speeds. I would get some real riding pants with hard armor and abrasion resistance. They're more affordable and breathable anyway. I would only consider riding jeans for brief, backroad use. My Roadcrafter is my go-to. Best $1,000 I've ever spent on gear, no kidding.

For hydration, I have used a Camelback myself. I have a Throttlemeister, so taking my hand off the bar to use the drinking tube is never a problem.

The MP3 rack is sweet. Get it, no regrets.

I use a medium Motofizz bag that anchors to the passenger grab rails and the MP3 rack. Holds enough clothing for a 7+ day trip, multiple pairs of shoes, you name it. Awesome and durable, and pretty rain resistant even without the rain fly.

I always ride with an air compressor, tire repair kit, tool kit, and various zip ties and bungee cords. It all takes just a modest amount of room in one of my side cases.

Enjoy the trip! Avoid the 5 unless you're in a hurry. 1 is best (you can make the trip within daylight hours during the summer), 101 2nd best (about 2 hours longer than the 5).