Run a fit program, to make sure your reach isn't too great, assuming you can be fit on your bikes, then start with the seat. If you are too far forward, your peddling doesn't stabilize your position on the seat. If you are too far back, your ability to spin is a problem. Too high you feel a pain where the sun don't shine, and your knees lock out every turn of the pedals. Too low, and you feel you don't have any power, and it will seem like you aren't stretching out enough in the leg action. Tipped up too high, and it can hurt, tipped down too low, and you will slide forward all the time. But overall, work on the seat.
Wear nice fat cycling gloves, so you aren't unecesarily abusing your hands, and everything attached to them. make sure that your arms aren't locked out, that they are bent, and you feel agile in the seat.
Normally you want to see people spinning nice light gears at the outset, but if you don't have suspenssion, and the gears are two light, I find it a problem to get over the bumps with my legs.
Anyway, I don't think that a little bit of non-cumulative pain for the weekend cyclist is a big deal. When I went on my 2 week trip, I think I would have had the kind of problems you are refering to when I took a couple of hour rides. After a few days, I was stronger. These could just be normal aches and pains.