You don't need padding in your shoe. A cycling shoe and a walking/running shoe are different things completely.
Having your cleat all the way back is the way my wife's bike fitter set my wife up and suggested it to me. He said use your big muscles to ride, not your little ones. This is his website if you want to see who he is:
Bicycle Fit Guru ? The Midwest Premier Bike Fit Studio
I had the same fire/pain as you are describing, your shoes are too tight which compresses a nerve in your foot. The suggestion of the metatarsal bump may help too. My shoes are only tightened in the ankle area, everywhere else is loose (8.5 EEEE foot here).
I use the Icebug insoles Slim Medium. Why the slim? I don't have room to give up in my shoe already, why add more bulk. If you add bulk inside your shoe you will hurt more. Took me 2 years to find the right combo, and now that I am thinking about it I didn't even notice my feet on my last ride.
https://us-shop.icebug.com/collectio...le-slim-medium