Does the commander count as part of your deck?
Yes, the Commander is part of the deck.


  903.5a Each deck must contain exactly 100 cards, including its commander.


The Legend rule doesn't limit what can be present in a deck &mdash; it limits what's on the 'field &mdash; but the following Commander rule does:


  903.5b Other than basic lands, each card in a Commander deck must have a different English name.


The uniqueness rule extends to the sideboard. You only have a single copy of a card in both the deck and 10 card sideboard combined.