A long shot left depending on how much you have done. You continue the game after it has completed so you can 100% it. Its up to you i supose whether you want to do all the side missions, riddler trophies etc.
Little bit hard to say as they say that quite alot throughout the game. Without posting spoilers so you don't spoil it for the rest, what boss have you got to? PM me or at least make sure you warn people that a spoiler
will be below.
When Protocol 10 finally kicks in, it does spell the start of the final run for the main story of the game but there is still quite a chunk of it left to do, so depends if you just focus on doing that as quick as you can, but its totally worth sticking through..and
yes you can carry on the other side missions once the main story is done