Your position on your bike will use a slightly different set of muscles than your mountain bike probably does... You're probably fairly upright on your mountain bike and more leaned over on your road bike... The more leaned over position is probably using different aspects of your butt/thigh muscles than your mountain bike does... I'm guessing your probably using your butt muscles more with the road bike, but someone who knows the names of muscles could actually tell you what I mean But you probably are using a different muscle group than you're used to.

The road bike crank being shorter should be easier on your knees, and it should want to spin-- you're going to feel like you're getting more power on the longer cranks of the mountain bike, that you can hammer a bit more.

The big chain ring on the road bike is definitely a bigger gear than you had on your mountain bike crank.... The mountain bike has bigger gears in the back than your road bike does...

The road bike middle gear (39) is more like the 42 teeth on the big chain ring of your mountain bike and probably more similar to what you're used to riding.