Socks are important. In my opinion and experience, thick socks are usually problematic as they tend to loosen and rub and create blisters. I wear a super thin pair of socks that move with my foot rather than with the shoe.

Shoes - Ichoro recommends NB for wide toe box - I wear Asics, which also have a wide toe box (I wear 4e). Nike on the other hand tend to be narrow. Your foot swells a bit when you run, so going wider may help. It sounds like this shoe/brand may be new to you - I recommend you consider finding a shoe that works and stick that shoe in its newest version going forward.

Modification - Some below suggested tape or doughnut. That may help. Depending on the extent of what you need, you may be able to cut out the section of concern as well. Lastly, make sure you are not lacing up too tightly. Good luck!