I hope you wedged a piece of cardboard or something into the front brake lever before disassembling everything. Otherwise, you're gonna have another issue if that plunger popped out and shot into the unknown.
I didn't pull it that far apart. Just loosened the master cylinder clamps just enough to take the throttle apart. All I did was slide it inward on the bar a little further to keep it upright. Nothing went flying or anything.