See if there is a "RoadRunner Sports" store where you live- they are so great!
I was having those same pains- one day during a workout with my trainer I just collapsed, my foot couldn't take it- I had to sit down for quite a while it was so painful. Turned out I had tendonitis. Went to the doctor she tried to get these like $400 insoles and insurance said no (what a SURPRISE). So she recommended to try roadrunner sports. There is one about half an hour where I live.
I went in and they had me run on a treadmill for like 30 seconds, then step on this touch pad. They told me my arches were low and that I needed stability shoes since I tend to roll on my feet. They picked out the PERFECT shoes for me and I LOVE THEM.
It's been over a year and since I got the shoes (I just bought my second pair) and I love them. Yes it did cost me a pretty penny ($150 a pair) but I will never go back to cheap shoes again- my feet are too important. I also went and bought my husband two pairs and he loves the shoes as well.
Seriously haven't had an ounce of pain while working out since

Oh to add I also get the extra insoles and that with the shoes is $150 and i totally recommend getting them if they suggest it. I never have foot pain anymore- I went walking for like 8 hours once and didn't have ANY pain at the end of it- it was AWESOME!