It’s always hard to say when you have pain what the issue is especially without understanding your environmental loads previous movement history ect. I can say with reasonable confidence that aches and pains that develop from correcting foot position often go away as tissues “readapt” so you’re not unreasonably optimistic.

Remember your body has adapted to your previous behaviors and injuries you have the right idea of this being a “process” but it will be a slow process. It takes something like two years to reconstruct the fascias of your body so be patient and be consistent.

If you’re looking at getting into running two books I highly recommend are Ready to Run by Kelly Starrett. It has a lot of the same ideas as Deskbound but adds a few benchmarks to work towards before you start crushing miles. The second book Is Your Whole Body Barefoot by Katy Bowman. It’s an entire book that works on foot health, alignment/position and provides some more ideas on corrective strategies.

Good luck on your journey!