Does the squadron token spent to activate AFFM have to come from the ship with the upgrade card? I would assume yes, but since AFFM is activated outside the ship movement phase and the card does not state explicitly where the token has to come from, there could be an argument made that where the token comes from is not specified. Thanks in advance!

Yes, that ship has to have the squadron token by the beginning of the ship phase. But it doesn't matter how it received that token, as it could have gotten it from tokening a previous command dial, from a ship with Comms Net, Garm, Hondo, etc.

The card says "you" may discard the card or spend a squadron token. That may sound like "you" means you, the player, but take a look at the Rules Reference Guide.

• On upgrade card effects, the term “you” refers to the
ship that the upgrade is equipped to.

I hope that's helpful! This rule also affects how a lot of cards are played.