The biggest difference between your Gold Wing and your Indian Scout that affects long-distance comfort is the riding position.
You got monkey butt on your Indian Scout because of it's EXTREME FOOT-FORWARD RIDING POSITION!
A foot-forward riding position puts the vast majority of your weight far back on your butt cheeks and on your tailbone. Bad! Your thighs and the back of your upper legs take almost none of the weight in that position. That's bad from the get-go, and only gets worse the longer you ride in the position.
Yeah, it looks cool to be crusin' down the street with your legs sticking way out in front of you like the "Keep on Truckin" man from back in the sixties (Google it), but that's all about it ergonomically that's cool.
On your Gold Wing, with your feet much farther back and actually under your thighs, your weight is shared much more evenly between your butt and the back of your upper legs. Also, with your feet positioned there, you can lift yourself up off of the bike's seat now and then and reposition yourself a bit to change the load slightly. Just try to push yourself up off the seat with a foot-forward riding position. Very hard to do, if even possible.
Bottom line is that cruisers with foot-forward riding positions are good for two things only: 1. Looking cool. 2. Very young riders!
Changing the seat is not likely to help you all that much. Unless you move the foot pegs back about two feet you'll have the same problem.
Don't get me wrong, I love the looks of an Indian Scout. But, at 60-something, there is no way for me to ride one much farther than a 30 minute local jaunt.
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Having been a long time Goldwing rider, Gl1100, Gl1500 and Gl1800 I agree with most of what you said. However, I downsized to a Suzuki Cruiser (gasp) last year and while it certainly does have the foot forward riding position you describe it doesn't mean that the ride can't be improved from stock. I have enough experience with getting bikes to fit me and my riding style to know immediately that I needed handlebar pullbacks and an aftermarket seat. After installing these on my C50 the ride comfort was much improved, just like it would be on the Indian Scout.
77Gowing's main problem is he doesn't have enough experience riding to know exactly what he needs to improve his ride and believe me it can be improved. But not having ridden a scout, even though I want to, and not knowing 77Gowings dimensions relative to his bike its hard to make a specific recommendation. All I can say is it might be a costly experiment for him to find the right combination of aftermarket components to tame the ride on his Scout, but it can be done. Mustang has a terrific reputation regarding cruiser seating and after installing one of their products on my Suzuki I couldn't be happier. I can ride a 150 miles at a time on that bike without stopping which is a little less than the 200+ miles I could do on my Gl1800, although on an all day ride I try to force myself to stop every 80 to 100 miles because at the end of a 300+ mile day I'll feel better if I do.
One thing I can highly recommend is a drivers backrest. They improve the ride in so many ways, on a cruiser it will tend to lock you into a singular riding position so you're not sliding all over the seat. Also they allow you to relax your back muscles so you don't have to strain to maintain a good riding posture particularly on a long day's ride when you get tired and tend to want to slump. Additionally you can use a backrest to relieve the strain on your bottom by pushing back and up against the back rest to raise your bum off of the seat for short periods of time, you can't imagine how much relief this maneuver can bring, particularly on a hot day with monkey but setting in.
A Scout or any cruiser will never be a Goldwing which is designed from the ground up as a mile eating tourer but a cruiser can certainly be improved upon to make it a reasonable alternative even for a 66 year old rider like me.
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A good back rest or even a back support belt would help. At our age looks secondary to comfort. 
