So I went to the shop where I bought my boots and spoke with someone about my issue. They heated my liners and had me wear the boots for 15 min. to reshape them.
That weekend I got the same burning feeling.
Went to the podiatrist the following week and he diagnosed it as "Mortons Neuroma". Basically have an enlarged nerve in both my feet. Reading on the internet I have the exact symptoms described.
Not really sure what I will do now since the season is over and it only really flared up about 4 hours into riding. Hope this helps someone having the same symptoms. Go see the podiatrist.