Having just went through alomost 18 months with a foot issue (Morton's Neuroma) I feel like I can make some recommendations.

Cycling orthotics are indeed different than running and dress shoe orthics - thinner, some have metatarsal pad built in.

If you have health Insurance I strongly recommend a visit to a Podiatrist - who can determine what the cause of this pain is.

I do really feel your pain. Cycling is a major part of my life and keeps me happy. No cycling = bad times. I had to actually stop from the pain for a while until I found a podiatrist with a cyclist on staff - he's got a cycling biomechanics coach on his team and everything. Bad news is he is out of network for everyone - so I only got 75% back from his high fees. That being said - he knows what he is doing and will help you get better. The Guys name is:
Rock G. Positano ( I have no affilation with him) at Hospital for Special Surgery - he is anti surgery don't worry :)

I should say that I saw 2 other podiatrists (in network of course) who were not very helpful frankly.

There are a couple of things you should do right away (I didn't and I made it so much worse):

1)make sure your cycling shoes and street shoes are Plenty wide enough for your toes side to side.
2) Get mentally prepared to ice your feet after every ride spinning included.
3) get orthotics designed for cycling to go inside youir spinning shoes.
4) your orthotics should have a metatarsal arch that will help take the pedaling load off the ball of your foot and spead it out on your whole foot. (this is costly but key! or else you will keep inflaming them)
5) make sure your cycling shoes and street shoes are Plenty wide enough for your toes side ti side.
6) Some people seem to be able to get past it without surgery depending on how much and how hard you ride.

Good luck,

-Niko

sometimes trying a larger surface area pedal like a look can also help.
spd compatible LAKE sandals are great for giving the metatarsal plenty of room.