Aching soles

Get some basic platform pedals and ride in your comfiest trainers and see if you get the issue. It's most likely that it's down to the shoes being too narrow or too stiff.

Another option might be a trekking style SPD pedal that comes with a wider platform to support more of the shoe. I have these https://www.wiggle.co.uk/shimano-t8000-xt-mtb-spd-trekking-pedals?sku=10... on my road bike and they've been fantastic. I was getting numb toes even in summer but it's gone away with these. Plus you can ride in trainers/flat mountain bike shoes if you don't want to be clipped in all the time.

I get this occasionally with a tight pair of shoes unless I slacken them right off, try riding with them really slack or try another pair of shoes

This is fairly common. Essentially you're taking too much weight through your feet for too long. Every now and again, get your hands right onto the flats at the bottom of the drops, and push down. It will take the weight off your feet, and the cramps you're experiencing will subside.

My personal experience is that after  riding in comfort  for over 6 months with Shimano ME2 SPD Mountain Bike Shoes, my feet started aching at the outside of my foot, the bottom of my toes and the balls of my feet.it felt a bit like a burning sensation. hot foot?

The more i read researched the issue, the more I was going down rabbit holes looking at all sorts of expensive solutions from bike fit to wedges to fix Supination and pronation of feet, to really expensive shoes.

Eventually I bought a pair of relatively inexpensive DHB shoes in a larger size from wiggle (I think they are discounted regularly) and all the pain disappeared. They claim to have larger toe box.

I suspect my feet had expanded during the quarantine because I was not wearing shoes everyday to go to work.

Please let us know how / when your issue is resolved.

With such a sparse amount of information to work with, it's nigh on impossible to give a definitive answer as there are so many variables to contend with.

However, if it is the outside of your feet that are aching my first thought would be that your shoes are too narrow. Most manufacturers build their shoes onto soles that are all the same width to keep production costs down. Fine if you have small, narrow feet, but a right pain if you are anything outside the typical build of their target audience. Being a big lad, well over 6 feet, I've always struggled for correct fitting shoes from the mainstream makers, the vast majority are far too slim.

There are a few exceptions though, Bont and Lake make shoes in wide fittings, with soles up to an EE width IIRC, but are quite pricey. Alternatively Bontrager make shoes with more fabric in the uppers allowing the foot to spread out over the confines of the narrow sole.

A common mistake that many riders make is fastening their shoes too tightly, especially close to the toebox, so if your shoes have laces, a strap or a BOA ratchet ease the pressure off closer to the toes allowing a bit more wriggle room.

Lastly, don't have your cleats too far forward in the slots. Ideally, the cleat should be under the ball of the foot, but too many cyclists fit the cleats too far forward where the metatarsals join the ball of the foot resulting in bruising and nerve damage/pain.

My advice would be to watch a few videos on Youtube, say Global Cycling Network for practical advice on how to set up your shoes to be as comfortable as possible.

Ouch. Tricky one; could be lots of things. Tight shoes? Your feet will swell a little as they warm up.

Try concentrating on where exactly you're pressing as you pedal: does it feel like it's in the right place or would you ideally move your foot a little bit to get the best position? If the latter, try adjusting the cleats accordingly.

Are you trying to turn too big a gear and pushing too hard? Try using a lower gear that enables you to pedal quicker but with less force on each stroke.

Finally, it's going be difficult to get a bike fit at the moment, but if you know an experienced cyclist it might be possible to ask them to watch you from a suitably safe distance. They could point out any obvious changes they felt were worth making.

Had similar issues when I tried clipless pedals. Pain when riding was tolerable but the awful cramp on the outside edges of my feet as soon as I stopped and which lasted for a few minutes was really bad. Had a bike fit and still got the pain. Tried moving cleats around, cleat wedges and insoles.

Tried some mtb shoes and pedals too just in case - still the same.

Gave up and stuck with flat pedals.

To be honest I never felt the supposed benefits of being clipped in, and I welcomed back the simplicity of flat pedals and the ease of stopping at lights and junctions.

Get a bike fit.
Also do you have wide feet?
Think a lot of cycling shoes are narrow. I'm an E width which isn't crazy wide but I had been squeezing my feet into some specialized shoes that were too narrow for years, this was pointed out to me at a bike fit, switched to some lake shoes (not the wide version, the non wide are wider than most) and haven't had any issues since.