I tried attaching a copy of my savefile, but it exceeds the maximum 5mb file limit, here are links from Dropbox:
=0 Memory Card (Save is set to in town before the "???" Trouble is accepted, if you want to continue from here go to the Trouble Center in town and re-accept it, talk to the masked mouse, and then travel to Hooktail Castle)
=0 Savestate (This is set to inside Hooktail's Castle where I most recently found Koops acting up. Mario is staged right beside a switch that needs activated by Koops after holding down the assist button and moving Mario to the top of the nearby yellow elevator)
=0 Laststate file (this is located in the same file as the Savestate, in case it is important)