The jb will survive Amazon firmware updates, its 'viral'.
It is generally a one way trip, unless you have the rescue pack installed (optionally, with the coward's rescue pack addition also installed).
Yes, <- the most general, all inclusive answer (there are exceptions that don't matter).
Put all of the update_*.bin files you used in /mrpackages, select KUAL menu: mr update.
MrPI will take care of them all in a single batch.
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