One or all could be a factor... (do not know if shackles have any effect on ride)
tires...
"big" (and heavier) tires could / will provide a harsher ride. A load range c (think these tire codes May gave changed) tire (light truck) will ride harsher than a load range b ("car") tire -- not that I would ever recommend a "car" tire on a Scout II.
Aspect ratio will also make a difference -- 70 will be slightly harsher and 60 / 55 / 45 will definitely be harsher (on our "old" suspensions not designed for such tires).
Springs -- probably designed for a gvw of 6200 lbs -- a very slim possibility: leaf springs "move" against each other as they flex. If yours are "sticking", I would assume the ride would be harsher.
You can get springs with different spring rates, but you still need to have springs that "support" the weight (including fully loaded) of the vehicle.
Shocks -- shock valving (bounce / rebound rate) -- shocks have different valving based on the vehicle and cover the variations from an unloaded vehicle to a fully loaded vehicle ("sprung" weight vs "unsprung" weight) - and what could be called "standard" shocks and hd shocks.
On our vehicles, it is mostly a "one size" fits all shock from the aftermarket world now. But, originally, my t/a had different shocks (IH part numbers) front and rear - meaning they were probably valved differently.
Do not know about rancho shocks / do not know if they have a specific Scout II shock. You might "try" a shock with different valving, if rancho provides such.
You can have shocks custom valved (Bilstein, koni, maybe rancho, maybe other off raod shock suppliers), but the price goes way up.