Awesome! The first post has now been updated to include that story. Again, thanks for the help.
I started thumbing through Shell Shock and noticed an Usagi Yojimbo crossover I didn't even know existed!
I started a thread asking if there were any Usagi crossovers besides Turtle Soup (one shot), Usagi Vol. 1 #10 and Usagi Vol. 2 #1-3 and I was told I had em all (despite Raph saying Leo and Usagi had met three times before "Shades of Green").
Looks like this one is quite obscure. Can't wait to read it.