I think your body has just gotten stronger and more fexible over time. Your muscles are adapted to the long low road bike position. Sounds like you can move your seat back a bit and it might give you more peddling power to boot. This is GOOD!
Try small changes with time between each change to adjust.
Move your seat back 1/2 inch and up a 1/2 inch. Then ride it for a week or two and see how you feel.