Riding long distances comfortably has very little to do with whether you're on a 'road' frame or a 'trekking' frame and much more to do with the tires you're using and the seat you're sitting on. Wide, plush tires will go a long ways toward absorbing the bumps in the road, and the seat is your most important point of contact with the bike.

For starters, try swapping the seat from one frame to the other, swap out the tires for wider touring tires, and see if your problems don't go away.

Riding long distances comfortably has very little to do with whether you're on a 'road' frame or a 'trekking' frame and much more to do with the tires you're using and the seat you're sitting on. Wide, plush tires will go a long ways toward absorbing the bumps in the road, and the seat is your most important point of contact with the bike.

For starters, try swapping the seat from one frame to the other, swap out the tires for wider touring tires, and see if your problems don't go away.

Edit: and for Pete's sake, make sure the bike fits you. If it doesn't fit you, nothing else really matters. Have a professional fit performed if you need to.