Cam – is there a reason why you have wood at grade level? Has there been landscaping done where fill was brought in? I’m not sure what you have for building code, but just about everywhere I have built, code requires that the foundation (concrete - or pressure treated wood in some areas) extend a minimum of 6” above grade. The problems you’re having is why this code is in effect. If I were bidding this ‘repair’, I would need to know more about what’s going on, what was done and why. I would have to excavate under the door and to the right / left about 12” or so to see what the heck the builder did. I would then use a combination of water shield and mastic to seal the exposed area, then I would grout over that up to the door threshold. After the gout has set, I’d run the pavers up to and under the threshold. That would be roughly one day’s work.
You shouldn’t have to remove the door unless the leading edge of the actual door frame is unsupported. If the builder did things correctly, he/she would have put liberal amounts of caulking under the threshold to seal it to the seal plate. The pictures look like the threshold is a scabbed on chunk of aluminum with a bunch of caulking slobbered all over the place. You may be able to just yank that off without removing the door. Whatever you have there, that leading edge needs to be supported by something, whether it be the pavers or a board screwed to the foundation.
