OK, I got icons working as well.
I have managed to get a game fully working with Admob plugin and ads are showing. Everything is working great. I'm going to try uploading to Google Play and see how that goes.
Uploaded to Google Play with 0 issues. Same game, but here are some Build size differences.
Old CocoonJS Compiler - 11.3mb
Intel XDK Compiler - 20.8mb
CocoonIO - 8.1mb
Game boots up faster than old CJS and has no screen flickering.
Issues found that might help others.
1. This game is older and does not need WebGL. Turned it off in C2 before exporting and the game scaled correctly.
2. The whitelist plugin that is installed by default in Cocoon.io caused my game to not load. Uninstalling it from Plugins fixed that error. Ludei has confirmed that plugin does not work with Canvas+
3. Icons work by following the template linked above and adding the appropriate lines in your config.xml as seen in the cocoon.io docs. https://cocoon.io/doc/icons_and_splashes
Later today I will test with iOS.
Final note, I am doing all testing with Canvas+