Hi Mekon.. hope this will help as I thought about this going the other way to flats..
Aching legs, I think that riders on flats have their feet on a bigger pedal and possibly their contact point is further back on their foot, if you follow. Even using their instep are a sometimes on steep stuff. Leg muscles will adapt... My feet were really aching with soft shoes on flats in the beginning too.
I did a day with Andy Weir coaching on a topic and he noted that a fair few of clipped riders spend more time with their heels up, even when descending.. I now make a deliberate effort to keep heels down. Have a think about how you rode flats and get your feet in the same position.
When you have cracked it, you qualify to argue on flats vs clips threads ! It makes me laugh sometimes when flats riders are looking for sticky shoes that feel like they are stuck to the pedal.... like clips then !