a) None, unless you have our jailbreak in-place
None, even with the jb in-place, unless you use one of our blocking tools
b) Under investigation.
c) you lose the ability to nest collections, you gain the ability to use cloud collections.
Yes, if jailbroken and using LibrarianSync.
Plus, there are alternatives to Calibre when using LibrarianSync.
Possibly the easiest to use is LibrarianSync's ability to build the collections database from the file tree structure.
(KOreader already uses the file tree structure - to a Kindle, the world is flat (the file tree got run over by Lab126's fork lift) - but LS can fix that.

)
d) LibrarianSync
Note: Your device must be registered to use collections.
Translation:
Stay with your 5.4.0 and use something other than your Kindle to contact Amazon with -
at least until we sort out a more elegant solution.
There are a lot of users with the same requirements as yourself right now.
Being locked out of the newest Kindles for better than a year lost us a lot of contributors.
Now that we have access to the newest generation devices, we are picking up contributors again.