-This .cap had two problems. The first one is that the character would jump while in idle position. The second is that the character would jump while shooting.
-After examining the event code, there was no reason why the unwanted jumping was happening, and so I diagnosed it as a glitch.
-The glitch appeared to be caused by the "idleNshoot" and the "jump" animation tier. So I removed those, and then put them back in fresh.
-I took all of the event codes you had, and made some new ones, and compiled them all into one event sheet.
-I then took all of the events and separated them into two groups: One group for the basic run/jump/idle animations, and the second group for shooting.
-I saw what you were trying to do with the wait object, but the input method was ineffective because it wasn't attached to another event. So, in order to get the 'idleNshoot' animation tier to play when you press the 'control' key and hold itself for a period, I used the function of enabling/disabling groups. When you press 'control' it will stop the run/jump/idle group animations and commands from playing, and the wait object will cause things to delay for 500ms and then 'run/jump/idle' group will be enabled. This happens very quickly. This also allowed me to get the shooting animation timing to be closer to what it looks like in MegaMan, but you'll have to tinker around with it to get it just right to how you want it.
You might also consider using the Wait object to duplicate the MegaMan shooting limit (I believe you can only shoot 3 lazers shot for a period and then you have to wait for a short period before you can fire again, but I'm basing that on the NES version).