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If I start my turn with 3 Attack Drones and a Sparring Gear on General Megatron, does that count as 4 Upgrades (Meaning each Attack Drone counts, and therefore trigger his ability), or only 2, since only 2 slots are filled?

Yes, each Attack Drone counts individually, so that is 4 upgrades, triggering General Megatrons bot mode ability.
Source: Wizards of the Coast (2019-05-28)    【Link to Ruling】
Tags: General Megatron, Infantry Leader