ok lets face it, you are on your trip now, so it is what it is--but seriously, this is why you NEVER change out stuff right before a tour. Its just asking for trouble, same with all self propelled activity, you're the old hiker guy right? It would be like taking new boots and diff socks right before a long multi day hike...

here's the deal, with saddle height changes, fore aft changes, spd cleat changes, its often just a small change that can make a difference, and cleated pedals vary in how they hold the shoe--some have more "float" than others, free play side to side, and others dont, which cna be a real factor just that.

I wish us internet dudes could help you, but frankly without seeing in person what you had before to help in person set up your new stuff, its kinda out of our hands.
If at all possible, if you dont have that much experience setting up pedals, seat and all that jazz, try to visit a bike store and hopefully a knowledgeable employee (not the 22 year old kid) can at elast set you up in the ball park.

the other kicker here , is that touring on a heavy bike for hours on end WILL show up any misfit, and yes, you can bugger up your knees, dont screw around with this. We gotta take care of these old knee parts of ours....
good luck and listen to your body, adjust stuff logically and in small amounts each time. Try to get the feeling your bike was giving you before. Downshift and keep torque low on the knees, seriously.