The SkullOwner string is replaced with a SkullOwner compound. You cannot the string for detection as a result.
You're detecting a root item tag called "damage" declared as an integer, which doesn't exist. The correct tag is "Damage" (as tags are case-sensitive) and the datatype is short.
Enchantment IDs and levels are normally stored as a short, and item data you provide is typically not auto-corrected and will remain integers as you've defined. You should declare them as short instead, so that any detection method you're using to detect enchantments will work for every method of application.
And finally, you have also closed the tag compound, and then opened an unnamed compound after it, breaking syntax.
What you should do instead is assign a custom tag to the item being provided, and then detect that item based solely on the custom tag. That way you don't have to fiddle with detecting every single tag on the item, which will break if you need to change any of that data.
For example, the following provides an item with a custom byte tag called SKULL with a value of 1.
/give @p minecraft:skull 1 3 {SKULL:1b,SkullOwner:"xXElite_PythonXx",Unbreakable:1b,display:{Lore:["_____"]},ench:[{id:0s,lvl:31073s},{id:7s,lvl:31073s},{id:4s,lvl:31073s},{id:3s,lvl:31073s}]}
And the following labels the player if they have it in their inventory:
/scoreboard players tag xXElite_PythonXx add skull {Inventory:[{Slot:103b,tag:{SKULL:1b}}]}
Then you can go back and modify the /give command as you'd like without changing /scoreboard (provided you do not modify SKULL).
Create scoreboard wSkull: scoreboard objectives add wSkull dummy
[1]Repeating command block: scoreboard players set @a wSkull 1 {Inventory:[{Slot:103b,id:"minecraft:skull",tag:{display:{Name:"Leafy Headdress",Lore:["[Rare] [Quest Item]","Some irritating thorns poke out of it."]}}}]}
[2]Repeating command block: execute @a[score_wSkull_min=1] ~ ~ ~ [command you want to happen when the custom head was worn]
At [2]Repeating command block, you can do multiple of these if you want alot of things to happen whoever wears your head.
Slot:103b locates where the helmet should be put when you want to wear it inside your inventory.
Best Answer
For
/clear, it's/clear <player> <item> <damage> <count>rather than count before damage, as is the case with for example/give, so it should be/clear Diamondman211 skull 3 1 {SkullOwner:Bacon}