Yep....in the year I've been riding my road bike, I feel that in getting slowly more comfortable, half the changes were things I did to my bike, and the other half were things my body did to adapt to riding my bike.

Also, it took several months for some little things to make themselves obvious to me about something about my bike fit that needed changing. I didn't know how I was "supposed" to feel. But as time went on and I kept riding some things just began to jump out as needing a change.
At first I felt I needed a really short stem and my saddle shoved all the way forward to enable me to reach the handlebars and not feel I was falling on my face with weight on my hands.
As I got stronger over the months I swear my body also stretched and I felt cramped and too far forward. I then put a longer stem back and shoved my saddle all the way back and it made my reach EASIER and now I feel really comfortable and my weight is better balanced further back. Go figure!