I have an enclosed deck that is basically worthless. It has a metal roof and bakes in the summer (and spring and fall for that matter) making it way too hot to use, and leaks in the winter (and retains no heat). I'd much rather convert it into an open deck. There are a few obstacles I have to get through first.
Edited to include only The first question here:
1 – While the pier is anchored in concrete, that concrete is below the level of the dirt. 
In this images the dirt around the pier is on top of concrete, however you can see the wet area where the dirt was and the the wood is beginning to rot. Will I need to replace this pier (and thus, all the rest) or can I pour concrete around it in a sonotube?
Best Answer
You'll need an engineer to tell you if those posts have enough good material remaining. But one thing you can do is figure out if your post sizes and spacing is over-built for your local codes. You'll have to find the codes for your area.
Here is an example of deck specifications.
If they are OK, you'll want to re-grade and treat them to prevent more rot.
If they are not OK or you just want them to look better, you can cut off the bad portion and pour new (higher) footings. (Make sure the footing depth and diameter and height above grade meet local code) Make sure you cast a metal post base in the footing. Don't cast the wooden post in the footing.