I've always walked with my toes pointed slightly out (opposite of pigeon toed) and I bought clipless pedals a year ago. Whenever I use them my ankles hurt - especially the right. Is it a good idea to keep my cleats aligned straight and build strength/flexibility to pedal that way or should I toe them out until it's comfortable? If i toe it out to a more comfortable position the crank arm rubs the inside edge of my shoe as I pedal. For reference I'm using spd pedals and cleats. I have not put significant mileage on my clipless pedals for this reason but maybe I just need to htfu?

My advice is don't use a bicycle for orthopedic surgery. Pedal extenders so your feet don't hit the crank arms, and get a proper fitting.

Yes, get pedal extenders if needed. Or just move the cleats as far to the inside of the sole as possible while still maintaining the necessary angle. That will move your foot the the outside away from the crank arm. It is okay if the cleats extend over the edge of the sole a little bit.

Under no circumstances should you ride with your feet pointed in an abnormal position...for you.

I developed knee pains keeping my right foot straight. A pro fitter advised me to point the feet where they want to point and I haven't had any problems since then.

You need to move to Eugene. Lots of "Webfoots" around here

I had the idea of pedals keeping the feet straight. And that may help some.

However, different pedals have different amount of float. SPD cleats are rated for about 6° Float.

I believe the Speedplay & Speedplay FROG pedals are rated for the most float (I think the Frog is higher than the standard Speedplay).

Anyway, you might try the Speedplay pedals, and let your legs naturally choose their angle. As mentioned above, the pedal extenders might help with heal clearance.

It wouldn't hurt to also talk to a podiatrist with an interest in Sports Medicine (and cycling). There is lots of good information on the internet, and it is good for food for thought. But for specific medical recommendations, it is worth about as much as it costs.

Thanks for the advice everyone! I hadn't heard of pedal extenders before but I'll look into it. Do most LBS carry those or is it rare enough that I'll probably have to order online. Would rather buy local if possible.

You don't use float to give you the main angle you need. Only to make up for any errors in setting the cleats. IMO anyway. Try for the necessary angle and let the float take care of the small errors.

I agree that pedal extenders could be the right solution, but you should try to move the cleats as far inboard as they will go first. The only trouble with exptenders is that they put the force further out from the pedal increasing the torque on the crank arm threads. Some folks worry about carbon and even aluminum cranks breaking due to a lot of weight applied that far away from the connection point between the pedal and the crank arm. Of course moving the cleats inboard does pretty much the same thing just not quite as extremely.

Any local shop than does bike fitting should carry them.

If your feet point out slightly, as you say, then extenders shouldn't be necessary. First just reset your cleats so they aren't forcing your feet straight. You may be surprised what a big difference a small adjustment can make.

I use Kneesavers brand extenders. I toe-out and have big feet so it's the only way I can use clipless pedals. I have found SPD mtb pedals don't have as much adjustment or float as some other systems. Been using Look Delta pedals for decades. I put the cleat as far inside as it will go and twist it as far as it will twist.
Years ago before there were extenders I drilled my shoes to hang the cleat off the inside. At the time I was using Time pedals and they kept breaking. I had a guy make custom extenders for me and voila...

This cannot be overstated. You can really injure your knees.

Somewhere around 1967 I broke my right ankle running a QB sneak in college. It was never properly set. As a result my right foot point slightly out. I use Speedplay pedals and have had no issues.

This - pro fit has my right foot pointing out just slightly. It's how I walk, and go figure, it's how I ended up cycling without any pain.

I went through a few different pairs of shoes and I'm still kind of tinkering around with it. Probably this and saddles as the most annoying parts of cycling for getting 'em dialed in and comfortable.