Foot Pain after riding

Go over the basics:

1) Are the boots the correct size, and are they adjusted properly? Not too tight, not loose anywhere?
2) Do your feet hurt in all the same places that your condition would cause anyway? 
3) Have you had similar pain in other brands of boot? Everybody's feet are different. Maybe Fox just isn't your brand.

From skiing I've learned that good custom footbeds make a world of difference.  If the boots fit properly I'd add footbeds.  Ski boot footbeds are great (more firm), but hiking ones would probably work too.  Bike vibration can also be relevant.  My feet are sensitive to vibes.  My CR250R gives me foot pr0oblems after a long ride.  My much smoother Husqvarna 300 causes no such problems.  That's more numbness and tingling. 

Definitely try some custom ski footbeds like BikePilot mentioned.

Mortons Neuroma, I have it and super common with cyclists, not sure about moto boots, but years of slamming my foot into narrow cycling shoes caused it.

i suffered from Plantar Fasciitis many times over the years especially during my hockey playing days.  Get yourself a good set of insoles, i've had good luck with Super Feet Brand.

I actually just got a new pair for my work boots yesterday from the Red Wing Boot store.  They actually scan your foot and see which ones suit you best, for me i have a very high arch. 

Here's the scan i got from Red Wing yesterday.

Ugh Morton’s neuroma sucks. I got it in my left foot.  Been over a year. Realized too late my tech 10s were a size to small and too tight at my toes. Over the counter ortho inserts help with daily wear shoes but still not 100%. Cortisone shot did nothing. Getting old blows. 

This thing works magic for me.....   ...and it feels so good.

https://www.amazon.com/gp/product/B00SMJIYNG/ref=ppx_yo_dt_b_asin_title…

 This hits home for me, have a nasty pronation that caused plantar fasciitis going on a year now (just got my boots resoled) and new custom orthotics that really fix the pronation, just have to really pull the trigger and take a few weeks off work to let it heal I feel like it gets alittle better then I re aggravate it

The pronation thing can suck.  When my left shoe gets worn on the outside, like your boots here, my left knee will start hurting unbelievably.  New shoes(or soles), and the knee is fine.

With the Fox Instinct's, last generation, the middle strap is in an awkward location, and no matter how it's adjusted, either causes me pain on the top of my foot, or they're too loose.  That's unfortunate because apart from that, the boot fits like a glove.

As Falcon pointed out, not every boot works for everyone.

The SIDI's are incredibly comfortable.  They may be my next boot.

Right now, I'm running Tech 7's.  Overall, I like them a lot.  My one complaint is that the toe section is pretty tall, and that sometimes makes it difficult to shift.

I’ve worn work boots the majority of my adult life because of what I’ve chosen to do for a living an I had the same problem. A shoe store guy saw how my soles were wearing and suggested inserts. I got some made and they changed my life, my boots last twice as long, and my knee hasn’t hurt since.