As others have said, get some decent kit and practice. Also when I switched to flats I dropped by saddle just a little and that really helped make me feel more connected. Been back on flats for a few years now and don't ever even think about foot/pedal connection.
Re foot pain, it's probably the shoes. Not been on the mtb much this year and been doing a lot on the road. First time back on the trails recently and I did get a bit of a sore foot around where I push on the pedals which I'd never had before, though that was towards the end of about six hours of looping around glentress