If you’ve got decent shorts, then either the positioning of the saddle, or the saddle itself may be an issue.
Get your sit bones measured, and make sure the saddle you have is suitable.
As others have said try and keep the weight of your hands and upper body.
I find on long rides that doing stretches of my neck arms and shoulders help to stop any stiffness building up.
Once you have your position on the bike sorted, there really shouldn’t be too much need for MTFU presuming you are riding at a steady pace, and are eating and drinking properly.
Edit: Do you carry a heavy rucksack?