Sounds like your boot is too big (not just length but volume).
Whenever my arches ache it's because I'm riding toe side and have heel lift. And when you say they are packed out after only 5-6 sessions, it really confirms that the boot was too big to begin with.
The boots are very snug. Toes touching the end but when I'm strapped in, I do feel sone pressure on the sides. I tried loosening the ankle strap but its probably as "loose" as it can be without the boot moving. I may need wider boots if anything. How long would you say it takes for the boot to pack out? They were way too tight at first and I was going yo sell them but after the guy at the store said I need to wear them a few more times to be comfortable. My feet were measured at size9 and thats the size of the boot. Previous boots were way too big at 10.5 but no arch pain but I also didnt use superfeet. I had cramps in my feet for a few runs and it would go away.