It is unfortunate that you had four teeth amputated and no have these issues that could have been avoided by early expansion.
Consider the use of the DNA Appliance it uses very light forces and there is virtually no inflamation which causes pain and resorbtion and/or bone loss.
Shortened roots...
Orthodontic treatment will definetely close the gaps and correct the bite.Post orthodontics the crown will be in better shape and the bite will be uniform.
I don't recommend orthodontic treatment until you are ready to stop the thumb habit because it will likely be a waste of money. Continuing the habit will undue all of the work with braces or Invisalign, and a retainer will not likely keep the teeth in a good position.