Thank you. Moving the command up between the image tags and tile tags seemed to do the trick. The conditions below look to mostly work (there still does seem to be some type of issue with the "waist" commands.)
Regardless of the "waist" command issues, it still looks like the rule that Mesen cannot insert a replacement graphic larger than the target graphic may be a deal breaking issue for this strategy anyway. Below represents an effort to squeeze Samus into the available player squares.
In my opinion, crunching the legs into the available space makes the animation look a bit jarring since the sizing is noticeably different. Maybe it's just me, but playing with these changes makes the game feel worse than before. It's like the legs of Samus inexplicably transformed into the legs of a six year old child.
Ideal Jumping Graphic:
Alternatives that come to mind are as follows:
-Hack the ROM to add a new square below the bottom-rear of the player sprite (the front has sufficient space). Then, incorporate the change into the .ips file included in the pack.
-Hack the ROM to simply move the rear foot square (520,FF161927) so that it is now directly underneath Samus rather than out to the side. This would also need to be incorporated into the .ips file.
*This is not ideal as it would remove some of the customization options available to the player (like playing with 8 bit graphics but 16 bit sound)
-Find some type of workaround using additional conditions in Mesen.
*As a sidenote, I did attempt changing the x and y coordinates of the very last command in hopes it would move the block. Unfortunately, it seems to move the graphic within the fixed block rather than move the block itself.
-Throw hands up in frustration, walk away, and go out for bubble tea instead.
If anyone has the technical knowledge to pursue any of these alternatives, I would be happy to incorporate into the master pack
For now, it appears I may be stumped again.