What you outlined in #1 is correct.

• Harry Angel has a new face (the 3rd face you mentioned) since his head was injured in the war. That is Mickey Rourke's face. Toots Suite would not have recognized the new face because he never saw Harry after his injuries.
• However, Toots Suite might have figured out who he's dealing with since Harry tells him his name. Toots knows Johnny Favorite took over Harry Angel's identity since he and Johnny were together when they grabbed the real Harry Angel in Times Square.

Johnny ate harrys heart so it was always Johnnys body but with Harrys personality , then there was the facial reconstruction
you do not punish someone for having big boobs!

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No, he was damaged in the war afterwards and facial changes. Then Ethan and Margaret picked Johnny/Angel up out of hospital, dropped him back off at Times Square, and that was that.
Toots was pretty sharp. Angel approaches him and Toots immediately knows he's being investigated for the past.