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I would recommend concentrating on your abs, lower back, shoulders and neck. Do high rep exercises (12-20), three sets for each exercise. I'm sure you can find various exercises for these body parts somewhere on the net.
Your diet during the trip will also be very important, lots of water and carbs. I am not a nutritionist so I'll let you chose the foods but I'm sure you get my point.
FlyNavy:
2 things I have learned. First..Try a pair of those lycra type shorts that cyclists wear. Im serious. No Monkey Butt..no chaffing at all...more comfort by at least 50%. Second wear earplugs..Your mind has to process sounds and it wears you out over time. Plugs help. Try 12oz. curls..lol.
WallyBally
I think the abs/lower back /shoulder area are all good ideas. I would also focus on making sure you stretch your hips and hamstrings at each stop. Especially your hips, you would be surprised how tight that area can get and how much lower back discomfort can be cause by tight hips. A split squat position with an upper body twist is a good one. Off the top of my head the only other thing I can think of that helps me on long trips is frequently flexing leg and arm muscles to keep the blood moving.
The guy that states take a 300 mile ride and see what aches got it right. Building strenght and most importantly elasticity in your waste is good. Gold Bond body powder in your skivies will also help. Safe journey.
Get a medicine ball (they come in all sizes and weights these days, and some even have handles) and a Swiss ball. There is no end to the core workouts you can do with these two.
And if you can find a "captain's chair," those are effective, too.
Whenever you do any core workouts, stretching is equally important.
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