You don't include the date in your desired output, so I'm not sure if you want to use it for your stats or not?
Anyway, this should be fairly straightforward. stats lets you perform statistical calculations split by an arbitrary number of fields. Provided you have extracted the fields properly, I'm thinking something like this should work (without the date):
... | stats count by Company,Help_Desk_Agent,Customer#
If you want to include the date in the output, but not group by it, you could use stats values() :
... | stats values(Call_Date),count by Company,Help_Desk_Agent,Customer#
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