So I was having an issue where the inside of the heels of my shoes was rubbing on the chainstays thus wearing away the paint. This wasn't a constant rubbing but rather about every 10 or so revolutions I would feel a slight bump on one side or the other. I guess I'm not the best/smoothest cyclist.

I've had the paint touched up but figured I needed to try and correct the issue otherwise the paint would just keep wearing away. So, I moved the cleats on my shoes back effectively moving my feet forward.

The result was I no longer rub the chainstays but on my first ride I noticed 2 things:

1. The insides of my feet now occasionally rub the crank arms.
2. My knees started to ache after about 20 miles.

I decided to head home and ended with 26 miles but with aching knees and concern about rubbing the crank arms.

So now I need to decide if I should move the cleats back to their original position and try to consciously keep my shoes from rubbing the chainstays or is the aching just a short-term issue because I'm not used to the cleats in the new position. Not even that worried about rubbing the crank arms at this point as I figured sore knees was a more important issue to resolve.

Any thoughts?

How massive are your feet??

If you move the cleats back, you might need to drop your seat a bit.

Where do the cleats positioned relative to your feet?

You might be able to move the cleats laterally towards the inside of the shoe.

Small adjustments.

If you have a relationship with an LBS, they might be a better source of information because they can see what is going on.

Are you aware of Kneesavers? These are a short male-female extension that moves the pedals outward a bit.
Available from many sources, but here is one with a pic-
https://www.thethirdhand.com/Products/SC-PDA.html

Do note: using Kneesavers may require you to change the pedals and/or the cranks.
Some pedals only can be tightened with an Allen wrench (through the crank end hole) because they have no flats, and there's no way to tighten such pedals into the Kneesavers.
The other issue is that some super-light cranks have broken when used with kneesavers.

You walk with your toes pointed outward not inward, correct?

I never really looked but probably.

If the only thing you're worried about with your original cleat position is a bit of paint wear, then a small piece of clear packing tape over the chain stay in that area will protect the paint and be nearly invisible.