Sounds like you've taken a lot of steps to try and alleviate your pain but have you actually seen a professional about it? You mentioned custom orthotics so that let's me know you've at least seen an orthotist which is good but how about a physical therapist, podiatrist or ortho who specializes in feet?
You definitely took the time to explain and describe your condition but there are a lot of other factors that are omitted such as your current age, weight, posture (flat footed vs. extremely high arches, structure of your feet/ankles (ankle mobility/sub-talar mobility, Achilles tendon flexibility, what other activities/condition aggravate your discomfort, what relieves it etc. which all could have an effect on your pain.
But you didn't ask for a lecture on going to see a health professional so with just your description it sounds a lot like plantar fasciitis.
Google treatment for plantar fasciitis and follow the most common therapies and see if that helps.
Also, I'm sure the person who made the orthotics for you probably instructed you on a wearing schedule because if you simply stuck it in for the first time and used it for several hours right off the bat, that's only asking for more pain.