I had the same problem. Right foot is OK. Left just bumps in the shoe. I tried custom insoles, bike fitters … nothing. Finally I found Brannock Device in one bikeshop (the staff didn’t know how to use it) and solved the riddle. Yep. It’s heel to ball discrepancy. My feet length (heel to toe) is 280 mm (size 44). But according to Brannock Device while 1st metatarsal on right foot is 45 size the left foot is 46. The instability and pain in the ball of the left foot caused by lack of support behind the metatarsals. Metatarsal pads, valgus wedges and other stuff not works because the whole arch should be corrected. On insole bottom I added a shim (Sugru) in area between navicular and metatarsals to fill the void and problem vent gone. Note that this was done with custom hard insoles (Solestar) with very low flex. Size up the shoes also solves problem. But I have short toes and shallow feet and larger shoes is too big for me.