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EntityPlayer::func_192028_j aka EntityPlayer::playShoulderEntityAmbientSound is called every tick in the EntityPlayer's code. What this does is tell a shoulder-mounted parrot to play a sound. Not sure if Pixelmon even have parrots (or pixelmon that make use of the parrot's shoulder-sitting-ability)... The server-owner needs to either delete the player's data (easy solution), or edit said data with NBTExplorer etc; find the mounted parrot(s) under the shoulderEntityLeft & shoulderEntityRight tags respectively, and delete them.

williewillus is maintaining a primer on the 1.13 changes here: https://gist.github.com/williewillus/353c872bcf1a6ace9921189f6100d09a It'll be significant work for modders but I'd say considerably easier than 1.7 -> 1.8 was.

Maybe I don't understand everything you're doing but can't the capability system help here? It is exactly intended to adding "common" functionality including to vanilla things. Items themselves aren't ICapabilityProviders but ItemStack is. Seems like you should be able to make a socket capability.