it is a all new engine, but you could increase a 998 cc engine to 1043 cc and it would not be a new engine.
the 03-06 Z1000 is a ZX9R engine punched out and a cyl head re design.
I don't even know if there are crank swaps for bikes that make them a stroker...... like the 350 chevy's w/ a 400 crank.It will still be nothing alike.
the 2010/11 motor has a longer stoke for better midrange power, that's where the extra cc's went.
when you bore an existing motor you keep the same length stroke with wider pistons.