The stock seat will make it rough, but having comfortable underwear can minimize the butt burn. Get some made out of nylon and polyester. Cotton actually becomes abrasive when you sweat. If a new seat is not in the plans think about a gel pad. It is not as comfortable as a Sargant seat, but its better than just stock when you've been on the bike for 12 hours and you still have another 4 to go.
Get a throttle lock, if you don't already have one. Some are only $25 and work fine. Being able to change positions slightly helps with long-distance comfort. If you don't install highway pegs, think about frame sliders. Depending where they are mounted, they can provide a temporary foot perch and relief.
Bring Advil and Tylenol. They work differently so you can alternate taking each without overdosing on either. Remember to eat something with them and hydrate frequently. If you don't have to pee every 100 miles or it's dark when you do, you're probably not drinking enough. It is one of the most common contributors to early fatigue on long-distance rides.
If you are hurting after 400 miles, 900-mile days will be killer. The pain killers will help, but think about allowing an extra day for the trip. Covering 600+ miles a day will be tough enough. Even if you are doing mostly Interstate, you'll likely average less than 60 mph with the frequent and increasingly longer stops. For planning purposes, I usually use 50 mph average for long trips. The best I've ever done on 600-mile + days is 58 mph average on my FJR with a custom Russell seat and cruise control.
At 50mph average you'll need 12 hours to cover 600 miles. That's a good days ride and a safe one. 900 miles take around 18 hours. It's the last 6 that are killer and unsafe. If you start at 8 AM you'll need to go to 2 AM. By the time you check in to a motel, sleep, 3S, and pack to go it's 10 AM and you have to do it all over again, except this time you are still sore from sitting on that torture chamber for the first 900 miles and the last half of your day will be at night. When you need to pay attention the most, is when you will be the most fatigued and sore.
If you gotta do it, follow the link above to the Iron Butt Association's tips for LD riding. They helped me prepare for my long-distance rides.
Good Luck!
Mike